Variant report

Variant	rs7956480
Chromosome Location	chr12:122817507-122817508
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	chr12:122707881..122710843-chr12:122815945..122817819,2	K562	blood:
2	chr12:122709077..122712045-chr12:122816425..122818444,3	K562	blood:

Variant related genes	Relation type
ENSG00000184047	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10161534	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10734915	0.91[CHB][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10734918	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10744192	0.81[ASN][1000 genomes]
rs10744208	0.81[EUR][1000 genomes]
rs10744209	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10744210	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10744211	0.94[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10773075	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10773088	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10773103	0.94[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10773104	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10773152	1.00[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs10773167	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10773208	0.87[CHD][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap]
rs10846664	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10846688	1.00[CHB][hapmap]
rs10846699	0.94[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10846746	0.92[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10846764	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10846792	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10846830	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10846921	0.89[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.80[TSI][hapmap]
rs10846978	0.87[CHD][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap]
rs10998	0.87[CHD][hapmap];0.87[GIH][hapmap]
rs11057786	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11057797	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11057882	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11058034	0.82[EUR][1000 genomes]
rs11058226	0.89[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap]
rs11616082	0.82[EUR][1000 genomes]
rs11836188	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12369858	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap]
rs12372756	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12581249	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1473553	0.87[CHD][hapmap];0.87[GIH][hapmap]
rs1553179	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1803290	0.92[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1818050	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1973463	0.92[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2062488	0.84[CEU][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs2173582	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2341439	1.00[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28730465	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34129612	0.81[EUR][1000 genomes]
rs3817011	0.84[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4039670	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4758643	0.92[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4758648	0.94[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.80[TSI][hapmap]
rs4758662	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4758666	0.94[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]
rs4758667	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4997380	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55834409	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6488933	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6488939	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6488951	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6488958	0.91[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6489002	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7135419	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7294559	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7301515	0.85[TSI][hapmap]
rs7314638	0.87[CHD][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap]
rs7397299	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7952868	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7953007	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964138	0.84[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap]
rs7969429	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7974262	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7975747	0.94[CEU][hapmap];0.89[CHB][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9988963	0.87[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7956480	B3GNT4	cis	cerebellum	SCAN
rs7956480	GATC	cis	cerebellum	SCAN
rs7956480	NME2P1	cis	cerebellum	SCAN
rs7956480	GTF2H3	cis	cerebellum	SCAN
rs7956480	RNF34	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122754600-122822400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr12:122770200-122821600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr12:122770400-122821800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:122775600-122833600	Strong transcription	Liver	Liver
5	chr12:122776000-122822200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:122780000-122827200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:122781400-122821400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr12:122785800-122827200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr12:122788200-122821200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:122791200-122841600	Strong transcription	Placenta	Placenta
11	chr12:122792400-122819800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:122794600-122832600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:122795800-122818200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:122797200-122822400	Strong transcription	Fetal Muscle Leg	muscle
15	chr12:122800400-122820600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:122804000-122817800	Weak transcription	Stomach Mucosa	stomach
17	chr12:122804200-122839000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:122806200-122821400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:122809600-122822000	Strong transcription	Fetal Intestine Small	intestine
20	chr12:122809600-122827400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:122809800-122820600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:122810000-122820800	Strong transcription	Fetal Stomach	stomach
23	chr12:122810000-122820800	Strong transcription	Osteobl	bone
24	chr12:122810000-122821200	Strong transcription	Stomach Smooth Muscle	stomach
25	chr12:122810000-122821400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr12:122810200-122820200	Strong transcription	Right Ventricle	heart
27	chr12:122810200-122820600	Strong transcription	Lung	lung
28	chr12:122810400-122821800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:122810600-122820000	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:122812400-122817600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr12:122812600-122819400	Weak transcription	Fetal Brain Male	brain
32	chr12:122812600-122820600	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr12:122812600-122820600	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:122812800-122817600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr12:122812800-122817600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr12:122812800-122817800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr12:122812800-122817800	Weak transcription	Pancreas	Pancrea
38	chr12:122812800-122818000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr12:122812800-122818000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:122812800-122818000	Weak transcription	Gastric	stomach
41	chr12:122812800-122820800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr12:122812800-122829400	Weak transcription	Fetal Heart	heart
43	chr12:122812800-122839400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:122812800-122839400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:122812800-122844000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr12:122812800-122850600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr12:122813000-122817600	Weak transcription	Brain Substantia Nigra	brain
48	chr12:122813000-122817800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr12:122813000-122818000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:122813000-122818000	Weak transcription	HSMMtube	muscle

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