Variant report

Variant	rs10875861
Chromosome Location	chr12:49097940-49097941
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	chr12:49096013..49099597-chr12:49108017..49110290,4	MCF-7	breast:
2	chr12:49090243..49092400-chr12:49096342..49098055,2	MCF-7	breast:
3	chr12:49095312..49098051-chr12:49108736..49111295,3	K562	blood:
4	chr12:49078444..49081393-chr12:49097132..49098901,2	MCF-7	breast:
5	chr12:49074052..49077254-chr12:49096800..49101145,7	MCF-7	breast:
6	chr12:49096349..49098245-chr12:49108578..49110236,2	K562	blood:
7	chr12:49075555..49077522-chr12:49096426..49100046,3	K562	blood:
8	chr12:49087869..49089619-chr12:49097319..49099589,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000139620	Chromatin interaction
ENSG00000129315	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10747554	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783273	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10783274	0.82[ASN][1000 genomes]
rs10783275	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10783277	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs10783278	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783281	0.88[EUR][1000 genomes]
rs10875849	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs10875850	0.87[ASN][1000 genomes]
rs10875852	0.92[ASN][1000 genomes]
rs10875853	0.92[ASN][1000 genomes]
rs10875862	0.98[ASN][1000 genomes]
rs1110432	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168657	0.85[ASN][1000 genomes]
rs11168665	0.92[ASN][1000 genomes]
rs11168674	0.89[ASN][1000 genomes]
rs11168697	0.90[ASN][1000 genomes]
rs11168698	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11168702	0.81[JPT][hapmap]
rs12299955	0.84[ASN][1000 genomes]
rs12426435	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1316514	0.96[ASN][1000 genomes]
rs1863541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1895995	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2114320	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2162317	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2277365	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2277366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2409085	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2898087	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3209584	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35717253	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3741628	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3741629	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3741630	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3741632	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3803025	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3943899	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4113946	0.87[ASN][1000 genomes]
rs4500528	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4760735	0.87[ASN][1000 genomes]
rs4760737	0.88[ASN][1000 genomes]
rs4760739	0.86[ASN][1000 genomes]
rs4760740	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6580689	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6580690	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6580692	0.83[EUR][1000 genomes]
rs6580693	0.92[EUR][1000 genomes]
rs7133756	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap]
rs7138190	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7138930	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs7139236	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7299276	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7304711	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7305907	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7306604	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7308699	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7314665	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7954446	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7954548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs7964546	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7966065	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7973824	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7974151	0.82[EUR][1000 genomes]
rs7974625	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7975030	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7975821	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9332441	0.91[ASN][1000 genomes]
rs9634241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9634242	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9634262	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10875861	ZNF641	cis	cerebellum	SCAN
rs10875861	SNORA2B	cis	cerebellum	SCAN
rs10875861	ADCY6	cis	parietal	SCAN
rs10875861	FAM186B	cis	cerebellum	SCAN
rs10875861	FLJ20436	cis	multi-tissue	Pritchard
rs10875861	WNT10B	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49076600-49109000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:49081000-49101000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:49081400-49104000	Strong transcription	Hela-S3	cervix
4	chr12:49081600-49099800	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:49081600-49103800	Strong transcription	Dnd41	blood
6	chr12:49081600-49107200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:49081600-49107600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:49081600-49108400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:49081800-49099400	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr12:49082000-49104000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:49082000-49107600	Strong transcription	Primary B cells from peripheral blood	blood
12	chr12:49082200-49100800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr12:49082200-49107200	Strong transcription	Liver	Liver
14	chr12:49082200-49107400	Strong transcription	Placenta	Placenta
15	chr12:49082200-49108000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:49082200-49108400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr12:49082200-49108600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:49082200-49108600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:49082200-49108800	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:49082400-49100200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr12:49082600-49107600	Strong transcription	Fetal Thymus	thymus
22	chr12:49082800-49101800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr12:49088200-49107200	Weak transcription	Small Intestine	intestine
24	chr12:49088200-49107400	Weak transcription	Psoas Muscle	Psoas
25	chr12:49088200-49107600	Weak transcription	Stomach Mucosa	stomach
26	chr12:49088400-49098000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:49089800-49109400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr12:49090000-49098000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:49090000-49098000	Weak transcription	Esophagus	oesophagus
30	chr12:49090000-49098000	Weak transcription	Fetal Kidney	kidney
31	chr12:49090000-49098400	Weak transcription	Ovary	ovary
32	chr12:49090000-49107200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:49090000-49107600	Weak transcription	Brain Angular Gyrus	brain
34	chr12:49090000-49107800	Weak transcription	Fetal Heart	heart
35	chr12:49090000-49108400	Weak transcription	Fetal Brain Male	brain
36	chr12:49090200-49098000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:49090200-49098000	Weak transcription	Brain Hippocampus Middle	brain
38	chr12:49090600-49098600	Weak transcription	NHLF	lung
39	chr12:49091800-49103400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:49091800-49104800	Strong transcription	GM12878-XiMat	blood
41	chr12:49091800-49107400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:49092800-49100800	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:49093400-49102800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr12:49093400-49108000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr12:49094800-49098800	Weak transcription	NHDF-Ad	bronchial
46	chr12:49095000-49099200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:49095000-49099800	Strong transcription	Fetal Intestine Small	intestine
48	chr12:49095000-49108600	Strong transcription	Fetal Stomach	stomach
49	chr12:49095200-49103400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:49095400-49100200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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