Variant report

Variant	rs10846664
Chromosome Location	chr12:122823777-122823778
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	chr12:122821893..122824534-chr12:122852571..122854340,2	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10161534	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10734915	0.91[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10734918	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10734924	0.88[JPT][hapmap];0.80[TSI][hapmap]
rs10744192	0.81[EUR][1000 genomes]
rs10744208	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10744209	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10744210	0.85[EUR][1000 genomes]
rs10744211	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10773075	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10773088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10773103	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10773104	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10773152	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap]
rs10773167	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10773208	0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs10846688	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10846699	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10846746	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10846764	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10846792	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10846826	0.80[AMR][1000 genomes]
rs10846830	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10846921	0.94[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs10846978	0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs10998	0.87[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs11057786	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11057797	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11057882	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11058034	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11058226	0.94[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs11058402	0.88[JPT][hapmap]
rs11616082	0.85[EUR][1000 genomes]
rs11836188	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12369858	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs12372756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12581249	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1473553	0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap]
rs1553179	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1803290	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1818050	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1973463	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2062488	0.89[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2173582	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2341439	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28730465	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34129612	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3817011	0.84[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4039670	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4758643	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4758648	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs4758662	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4758666	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs4758667	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4997380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55834409	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6488933	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6488939	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6488951	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6488958	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6489002	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7135419	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7294559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7301515	0.84[CEU][hapmap];0.91[TSI][hapmap]
rs7314638	0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs7397299	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7398014	0.81[EUR][1000 genomes]
rs7952868	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7953007	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7956480	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]
rs7964138	0.89[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs7969429	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7973869	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7974262	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7975747	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9788145	0.82[EUR][1000 genomes]
rs9988963	0.87[CHD][hapmap];0.88[JPT][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
rs10846664	RNF34	cis	parietal	SCAN
rs10846664	NME2P1	cis	cerebellum	SCAN
rs10846664	GTF2H3	cis	cerebellum	SCAN
rs10846664	B3GNT4	cis	cerebellum	SCAN
rs10846664	GATC	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122775600-122833600	Strong transcription	Liver	Liver
2	chr12:122780000-122827200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:122785800-122827200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:122791200-122841600	Strong transcription	Placenta	Placenta
5	chr12:122794600-122832600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:122804200-122839000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:122809600-122827400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:122812800-122829400	Weak transcription	Fetal Heart	heart
9	chr12:122812800-122839400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:122812800-122839400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:122812800-122844000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:122812800-122850600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:122813000-122839400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:122815200-122824600	Strong transcription	Brain Germinal Matrix	brain
15	chr12:122817200-122827200	Strong transcription	Brain Anterior Caudate	brain
16	chr12:122818200-122824200	Weak transcription	Psoas Muscle	Psoas
17	chr12:122818200-122838200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr12:122818400-122831000	Weak transcription	Pancreas	Pancrea
19	chr12:122818400-122852800	Weak transcription	Stomach Mucosa	stomach
20	chr12:122818600-122824200	Weak transcription	Brain Angular Gyrus	brain
21	chr12:122818600-122837000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:122818600-122844200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:122819600-122825000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:122819600-122825000	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:122819600-122825000	Weak transcription	Hela-S3	cervix
26	chr12:122819600-122831400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr12:122819600-122835200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr12:122819600-122835800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:122819600-122837000	Weak transcription	Thymus	Thymus
30	chr12:122819600-122839200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:122819800-122825000	Weak transcription	HMEC	breast
32	chr12:122819800-122825200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr12:122819800-122825400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr12:122819800-122825800	Weak transcription	Fetal Lung	lung
35	chr12:122819800-122831600	Weak transcription	Fetal Brain Male	brain
36	chr12:122819800-122835600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr12:122819800-122837000	Weak transcription	Colonic Mucosa	Colon
38	chr12:122819800-122837400	Weak transcription	Small Intestine	intestine
39	chr12:122820000-122824000	Weak transcription	Fetal Intestine Large	intestine
40	chr12:122820000-122824200	Weak transcription	K562	blood
41	chr12:122820000-122825200	Weak transcription	Fetal Kidney	kidney
42	chr12:122820000-122825400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr12:122820000-122825400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:122820000-122825600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr12:122820000-122826800	Weak transcription	Spleen	Spleen
46	chr12:122820000-122826800	Weak transcription	HUVEC	blood vessel
47	chr12:122820000-122830600	Weak transcription	Brain Substantia Nigra	brain
48	chr12:122820000-122831000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr12:122820000-122831200	Weak transcription	Gastric	stomach
50	chr12:122820000-122835400	Weak transcription	Dnd41	blood

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