Variant report

Variant	rs4310684
Chromosome Location	chr12:8143483-8143484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:8118275..8120504-chr12:8142781..8144500,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10732571	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MKK][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10846285	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10846331	0.95[ASN][1000 genomes]
rs10846333	0.95[ASN][1000 genomes]
rs10846366	0.82[ASN][1000 genomes]
rs11056779	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11056780	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11056782	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11056783	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11609309	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11611693	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12811781	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12813762	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12817051	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818249	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12818933	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12819689	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12820720	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12820845	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12823208	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12825574	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12831827	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4301853	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4628755	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883470	0.93[ASN][1000 genomes]
rs58279638	0.83[ASN][1000 genomes]
rs6488820	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7137199	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294894	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7299161	0.96[ASN][1000 genomes]
rs7299583	0.96[ASN][1000 genomes]
rs7313508	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313772	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958000	1.00[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7958511	0.82[ASN][1000 genomes]
rs7963223	0.95[ASN][1000 genomes]
rs7974225	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048545	chr12:7778760-8608231	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv541368	chr12:7778760-8608231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv430450	chr12:7853512-8146693	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1795892	chr12:7856819-8508693	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv2758292	chr12:7856819-8623987	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	esv2759877	chr12:7856819-8623987	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
7	nsv428270	chr12:7856819-8623987	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
8	nsv1054331	chr12:7924713-8183422	Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
9	nsv516107	chr12:7953089-8148099	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	esv1793008	chr12:7981374-8161231	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	esv1797934	chr12:7985460-8214261	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
12	esv1796684	chr12:7985489-8145133	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
13	esv1793572	chr12:7995827-8568422	Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
14	nsv557297	chr12:8000336-8143483	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
15	esv1792916	chr12:8000336-8171838	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
16	nsv469082	chr12:8000336-8171838	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
17	nsv469084	chr12:8000336-8171838	Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
18	nsv469085	chr12:8000336-8171838	Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
19	nsv469086	chr12:8000336-8171838	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
20	nsv557298	chr12:8000336-8171838	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
21	nsv541384	chr12:8003214-8188846	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
22	nsv1040972	chr12:8003413-8266291	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
23	nsv541388	chr12:8003413-8266291	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
24	nsv916941	chr12:8003501-8608220	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
25	nsv557312	chr12:8003758-8146162	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
26	esv2751118	chr12:8017473-8190206	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
27	esv2754110	chr12:8017478-8146689	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
28	esv2754825	chr12:8024363-8167542	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
29	nsv869752	chr12:8026388-8174912	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
30	nsv898729	chr12:8044997-8190206	Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
31	nsv1046432	chr12:8095522-8147177	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
32	nsv1045521	chr12:8123225-8242846	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
33	nsv898732	chr12:8123306-8190206	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
34	nsv1044509	chr12:8130958-8182060	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4310684	PRB4	cis	cerebellum	SCAN
rs4310684	CD163	cis	parietal	SCAN
rs4310684	HGD	trans	multi-tissue	Pritchard
rs4310684	CLEC4D	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8138600-8144400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr12:8141400-8143800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr12:8141600-8144600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
4	chr12:8141800-8144200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:8141800-8144200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr12:8142000-8143600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:8142000-8143600	Enhancers	Placenta	Placenta
8	chr12:8142000-8143600	Enhancers	Fetal Thymus	thymus
9	chr12:8142200-8144200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr12:8142600-8143800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr12:8142600-8143800	Enhancers	GM12878-XiMat	blood
12	chr12:8142600-8144400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:8142600-8144400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr12:8142800-8144400	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr12:8142800-8144600	Enhancers	Primary hematopoietic stem cells	blood
16	chr12:8142800-8144600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr12:8142800-8144600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:8143000-8143600	Enhancers	Primary T cells from cord blood	blood
19	chr12:8143000-8143800	Enhancers	Primary B cells from cord blood	blood
20	chr12:8143000-8144000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:8143000-8144200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr12:8143000-8144600	Enhancers	Primary T cells fromperipheralblood	blood
23	chr12:8143000-8144600	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr12:8143000-8144600	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr12:8143000-8144600	Enhancers	K562	blood
26	chr12:8143000-8144800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:8143000-8146000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:8143000-8146600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr12:8143000-8146800	Enhancers	Hela-S3	cervix
30	chr12:8143200-8143600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:8143200-8143600	Weak transcription	Stomach Mucosa	stomach
32	chr12:8143200-8143800	Weak transcription	A549	lung
33	chr12:8143200-8143800	Enhancers	Dnd41	blood
34	chr12:8143200-8144400	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr12:8143200-8144600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:8143200-8144600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:8143200-8144600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:8143200-8144800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:8143200-8147400	Weak transcription	HUVEC	blood vessel
40	chr12:8143400-8143600	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr12:8143400-8143800	Weak transcription	HepG2	liver

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