Variant report

Variant	rs7969019
Chromosome Location	chr12:31899733-31899734
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	chr12:31890682..31895418-chr12:31897600..31900050,5	K562	blood:
2	chr12:31880350..31888706-chr12:31898122..31903847,15	K562	blood:

Variant related genes	Relation type
ENSG00000151743	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10844000	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[YRI][hapmap]
rs10844002	0.87[ASN][1000 genomes]
rs10844003	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10844047	1.00[YRI][hapmap]
rs11051525	0.83[AMR][1000 genomes]
rs11051541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs11051545	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes]
rs11051555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11051559	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12367895	0.83[AMR][1000 genomes]
rs12813042	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs12813399	0.83[AMR][1000 genomes]
rs12813695	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35517071	0.82[AMR][1000 genomes]
rs4272861	1.00[CHB][hapmap]
rs7297921	0.83[AMR][1000 genomes]
rs7300260	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs7953551	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7960893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs7970737	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7978407	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3432694	chr12:31801467-32109828	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv898966	chr12:31810126-31944985	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
6	esv2422415	chr12:31863360-31930722	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv558100	chr12:31866833-32185924	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv1045464	chr12:31869888-32183792	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv541447	chr12:31869888-32183792	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	esv3363806	chr12:31872264-32410283	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
11	esv3508621	chr12:31872654-32410593	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
12	esv3508622	chr12:31872654-32410593	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
13	nsv558101	chr12:31876666-32006563	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
14	nsv1050448	chr12:31877289-31927006	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv558102	chr12:31889824-31907409	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv975473	chr12:31895430-31908180	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7969019	AMN1	cis	cerebellum	SCAN
rs7969019	C12orf72	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31885800-31900200	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr12:31889400-31905800	Enhancers	Primary B cells from peripheral blood	blood
3	chr12:31893400-31900000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr12:31893600-31905800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr12:31894400-31903400	Weak transcription	Spleen	Spleen
6	chr12:31895800-31902000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:31896200-31903600	Weak transcription	Fetal Kidney	kidney
8	chr12:31896200-31903600	Weak transcription	Small Intestine	intestine
9	chr12:31896400-31900000	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr12:31896400-31902000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:31897000-31899800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr12:31897600-31900000	Enhancers	Primary T cells from cord blood	blood
13	chr12:31897600-31902400	Enhancers	Hela-S3	cervix
14	chr12:31898000-31900200	Weak transcription	Fetal Intestine Small	intestine
15	chr12:31898000-31900800	Weak transcription	Colonic Mucosa	Colon
16	chr12:31898800-31900400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr12:31898800-31900600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:31898800-31900800	Enhancers	Primary hematopoietic stem cells	blood
19	chr12:31899000-31899800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:31899000-31900200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:31899000-31900400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:31899000-31900400	Enhancers	HepG2	liver
23	chr12:31899000-31900800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:31899000-31901000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:31899000-31901000	Flanking Active TSS	GM12878-XiMat	blood
26	chr12:31899200-31899800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:31899200-31899800	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr12:31899200-31900000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr12:31899200-31900000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:31899200-31900000	Enhancers	Placenta Amnion	Placenta Amnion
31	chr12:31899200-31900200	Enhancers	Stomach Mucosa	stomach
32	chr12:31899200-31900200	Enhancers	NHDF-Ad	bronchial
33	chr12:31899200-31900400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:31899200-31900600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:31899200-31900600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr12:31899200-31900600	Enhancers	HUVEC	blood vessel
37	chr12:31899400-31899800	Enhancers	Fetal Lung	lung
38	chr12:31899400-31899800	Weak transcription	Thymus	Thymus
39	chr12:31899400-31900000	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr12:31899400-31900000	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr12:31899400-31900000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:31899400-31900000	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr12:31899400-31900000	Enhancers	Dnd41	blood
44	chr12:31899400-31900000	Enhancers	HSMM	muscle
45	chr12:31899400-31900200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:31899400-31900200	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr12:31899400-31900200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:31899400-31900200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr12:31899400-31900200	Enhancers	Adipose Nuclei	Adipose
50	chr12:31899400-31900200	Flanking Active TSS	A549	lung

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