Variant report

Variant	rs10849578
Chromosome Location	chr12:997833-997834
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:990717..994064-chr12:994788..999202,4	K562	blood:
2	chr12:978470..980054-chr12:995425..998345,2	K562	blood:

Variant related genes	Relation type
ENSG00000060237	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10744729	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10849579	0.84[AMR][1000 genomes]
rs10849584	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11064580	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11064585	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11064593	0.94[ASN][1000 genomes]
rs11226	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11571409	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11571448	0.92[ASN][1000 genomes]
rs11611051	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11614499	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12581940	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12828016	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs2255390	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2269937	0.93[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286029	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748521	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4766370	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4980974	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6413436	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7296555	0.97[ASN][1000 genomes]
rs7300444	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7300718	0.94[ASN][1000 genomes]
rs7301931	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7303748	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7308979	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7310449	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7964502	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs953361	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541305	chr12:282465-1016828	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv869390	chr12:282465-1045994	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1044433	chr12:321619-1065402	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv541323	chr12:321619-1065402	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
8	nsv556890	chr12:662448-1100555	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS 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	58 gene(s)	inside rSNPs	diseases
9	nsv556892	chr12:673515-1210884	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
10	nsv898576	chr12:813411-1553450	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats 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	56 gene(s)	inside rSNPs	diseases
11	nsv948760	chr12:863833-1542875	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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	42 gene(s)	inside rSNPs	diseases
12	nsv1042333	chr12:907975-1081509	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv1052589	chr12:910460-1421493	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers 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	34 gene(s)	inside rSNPs	diseases
14	nsv1045278	chr12:920251-1697030	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS 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	46 gene(s)	inside rSNPs	diseases
15	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
16	nsv468960	chr12:975276-1455106	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
17	nsv556941	chr12:975276-1455106	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
18	nsv1044329	chr12:985144-1403020	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
19	nsv541340	chr12:985144-1403020	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
20	nsv1053198	chr12:993822-1034603	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
21	nsv541341	chr12:993822-1034603	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
22	nsv1041675	chr12:993822-1091354	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers 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	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10849578	RAD52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:962200-1002600	Strong transcription	Dnd41	blood
2	chr12:962200-1012400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr12:964200-1007600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr12:964400-1042200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:964600-1027200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:965800-1014000	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr12:965800-1028400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:966000-1002200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:966000-1012200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:966000-1014800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:967200-1005800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:968600-1006400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:980000-1013200	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr12:982200-1027000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:986200-1002400	Strong transcription	Left Ventricle	heart
16	chr12:986200-1042200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:986400-999800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:986400-1014800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:986600-999800	Strong transcription	HepG2	liver
20	chr12:986600-1012000	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr12:986600-1012000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:986600-1012200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:986800-1002000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:986800-1014600	Strong transcription	Primary B cells from peripheral blood	blood
25	chr12:986800-1028400	Strong transcription	Placenta	Placenta
26	chr12:987000-998800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:987000-999800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:987000-999800	Strong transcription	Brain Anterior Caudate	brain
29	chr12:987000-1000000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:987000-1000200	Strong transcription	Thymus	Thymus
31	chr12:987000-1000400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:987000-1000400	Strong transcription	HMEC	breast
33	chr12:987000-1001200	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr12:987000-1001400	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr12:987000-1001800	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr12:987000-1002000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:987000-1002000	Strong transcription	Duodenum Mucosa	Duodenum
38	chr12:987000-1002000	Strong transcription	A549	lung
39	chr12:987000-1002400	Strong transcription	Primary hematopoietic stem cells	blood
40	chr12:987000-1002600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr12:987000-1007000	Strong transcription	HUVEC	blood vessel
42	chr12:987000-1007200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr12:987000-1011200	Strong transcription	Liver	Liver
44	chr12:987000-1012600	Strong transcription	Primary T cells from cord blood	blood
45	chr12:987000-1014800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr12:987000-1017600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:987000-1020800	Strong transcription	Adipose Nuclei	Adipose
48	chr12:987000-1022400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:987000-1023600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:987000-1028400	Strong transcription	HUES48 Cell Line	embryonic stem cell

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