Variant report

Variant	rs2970532
Chromosome Location	chr12:25396035-25396036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:25393614..25397250-chr12:25537759..25541230,3	K562	blood:
2	chr12:25387866..25389921-chr12:25394570..25396396,2	K562	blood:
3	chr12:25387876..25389586-chr12:25395973..25398657,2	MCF-7	breast:
4	chr12:25390084..25393498-chr12:25395156..25398677,4	K562	blood:
5	chr12:25346926..25348461-chr12:25395724..25397256,2	K562	blood:
6	chr12:25393086..25399970-chr12:25400304..25404361,8	MCF-7	breast:
7	chr12:25395817..25398136-chr12:25402041..25404103,3	MCF-7	breast:
8	chr12:25392189..25396143-chr12:25537109..25540514,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000133703	Chromatin interaction
ENSG00000205707	Chromatin interaction
ENSG00000118307	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10842507	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10842508	0.92[CHB][hapmap];0.94[CHD][hapmap]
rs10842509	0.84[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10842511	0.86[ASN][1000 genomes]
rs11047809	0.93[GIH][hapmap]
rs11047826	0.85[CEU][hapmap]
rs11047877	0.81[EUR][1000 genomes]
rs11047880	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[EUR][1000 genomes]
rs11047882	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs11047892	0.92[CEU][hapmap];0.92[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs11047893	0.84[EUR][1000 genomes]
rs11047911	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11047918	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11533487	0.85[CEU][hapmap]
rs12228277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229161	0.85[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap]
rs12229450	0.85[CEU][hapmap]
rs12230737	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12230955	0.84[EUR][1000 genomes]
rs12423011	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12423489	0.92[CEU][hapmap];0.92[CHB][hapmap];0.82[EUR][1000 genomes]
rs12423778	0.85[CEU][hapmap]
rs12424283	0.84[CHB][hapmap]
rs12427119	0.85[CEU][hapmap]
rs12427141	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs17329424	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs17387444	0.85[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs3782188	0.85[CEU][hapmap]
rs3924649	0.92[CHB][hapmap]
rs4623993	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4963601	1.00[GIH][hapmap]
rs4963852	0.85[CEU][hapmap]
rs4963853	0.85[CEU][hapmap]
rs61016093	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61761101	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61763584	0.85[EUR][1000 genomes]
rs73073207	0.83[EUR][1000 genomes]
rs7309862	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7312175	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7973746	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7979296	0.92[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv898923	chr12:25357680-25397282	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv898924	chr12:25357680-25398972	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv557798	chr12:25359841-25397282	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv898925	chr12:25367669-25398972	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv898926	chr12:25367669-25408047	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv470279	chr12:25384658-25399121	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv898927	chr12:25389220-25408047	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	nsv522233	chr12:25392282-25397282	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25348600-25402200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:25348600-25403200	Weak transcription	Spleen	Spleen
3	chr12:25349000-25402400	Weak transcription	Right Ventricle	heart
4	chr12:25349400-25401800	Weak transcription	Fetal Brain Male	brain
5	chr12:25349400-25402600	Weak transcription	Brain Germinal Matrix	brain
6	chr12:25349600-25402600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:25349600-25402600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:25349600-25402600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:25349600-25402600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:25350000-25402800	Weak transcription	Ovary	ovary
11	chr12:25354000-25402400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:25354400-25402200	Weak transcription	Pancreas	Pancrea
13	chr12:25356600-25402600	Weak transcription	Fetal Heart	heart
14	chr12:25360800-25402200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:25361000-25402600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:25361000-25402600	Weak transcription	Fetal Brain Female	brain
17	chr12:25362000-25402400	Weak transcription	HepG2	liver
18	chr12:25372400-25402800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr12:25374800-25402600	Weak transcription	Placenta	Placenta
20	chr12:25375000-25402800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:25377800-25402200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:25377800-25402200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:25378800-25401800	Weak transcription	Adipose Nuclei	Adipose
24	chr12:25380400-25402200	Weak transcription	Fetal Lung	lung
25	chr12:25381200-25402400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:25382000-25402600	Weak transcription	Colonic Mucosa	Colon
27	chr12:25383000-25399000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr12:25385200-25402600	Weak transcription	Aorta	Aorta
29	chr12:25386200-25402800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:25386400-25402800	Weak transcription	Gastric	stomach
31	chr12:25386600-25402600	Weak transcription	Fetal Kidney	kidney
32	chr12:25386800-25402600	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:25387000-25396800	Weak transcription	Hela-S3	cervix
34	chr12:25388200-25397800	Weak transcription	NH-A	brain
35	chr12:25389000-25402200	Weak transcription	Right Atrium	heart
36	chr12:25389000-25402600	Weak transcription	HMEC	breast
37	chr12:25389200-25402000	Weak transcription	Fetal Muscle Leg	muscle
38	chr12:25389400-25396200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:25389400-25402200	Weak transcription	Psoas Muscle	Psoas
40	chr12:25389400-25402800	Weak transcription	Left Ventricle	heart
41	chr12:25389800-25400200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:25389800-25401800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:25389800-25402400	Weak transcription	NHEK	skin
44	chr12:25389800-25402600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:25389800-25402600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:25389800-25402600	Weak transcription	HSMMtube	muscle
47	chr12:25390000-25402600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr12:25390400-25401400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:25390600-25396200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:25390600-25398200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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