Variant report

Variant	rs610694
Chromosome Location	chr12:121304826-121304827
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121304739..121306957-chr12:121328981..121330571,2	MCF-7	breast:
2	chr12:120729252..120732032-chr12:121304408..121306982,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000202538	Chromatin interaction
ENSG00000200795	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs1027556	0.86[YRI][hapmap]
rs1039302	0.86[YRI][hapmap]
rs10431387	0.86[YRI][hapmap]
rs10437838	0.86[YRI][hapmap]
rs10774568	0.83[YRI][hapmap]
rs10774569	0.86[YRI][hapmap]
rs10774571	0.86[YRI][hapmap]
rs10774572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849786	0.81[YRI][hapmap]
rs10849788	0.82[YRI][hapmap]
rs10849791	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10849807	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849810	0.86[YRI][hapmap]
rs10849811	0.86[YRI][hapmap]
rs11065259	0.86[YRI][hapmap]
rs11065282	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs11065283	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs11065284	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11065293	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065298	0.86[YRI][hapmap]
rs11065300	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065307	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11065311	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11065322	0.86[YRI][hapmap]
rs11065324	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs1151849	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1151859	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1151862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11608262	0.83[ASN][1000 genomes]
rs11611087	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs1168944	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1168946	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1168948	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1168953	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1177585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1179939	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12371178	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12372231	0.85[ASN][1000 genomes]
rs12580949	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12809299	0.83[ASN][1000 genomes]
rs12822123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12825746	0.83[ASN][1000 genomes]
rs12831094	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13746	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1542859	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs1696357	0.82[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs1696390	0.84[ASN][1000 genomes]
rs1718180	0.83[EUR][1000 genomes]
rs1718188	0.85[ASN][1000 genomes]
rs2047568	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs2393717	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2393718	0.85[YRI][hapmap]
rs2461475	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2650017	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2701177	0.85[ASN][1000 genomes]
rs2701184	0.85[ASN][1000 genomes]
rs3213566	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3213568	0.86[YRI][hapmap]
rs3213570	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3213571	0.86[YRI][hapmap]
rs3213572	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs34009825	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34076777	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35600816	0.87[ASN][1000 genomes]
rs35706672	0.84[ASN][1000 genomes]
rs35905305	0.91[ASN][1000 genomes]
rs3809313	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3809314	0.86[YRI][hapmap]
rs3842985	0.81[ASN][1000 genomes]
rs3861797	0.81[ASN][1000 genomes]
rs3883901	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs3897746	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3901854	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs4454799	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs471688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4766979	0.84[ASN][1000 genomes]
rs4766980	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4767937	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4767941	0.84[ASN][1000 genomes]
rs487943	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs508595	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs520753	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531782	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs533264	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548452	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs572016	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs577961	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs580240	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58291418	0.83[ASN][1000 genomes]
rs58918988	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs590625	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs602984	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs608394	0.81[EUR][1000 genomes]
rs609700	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618482	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61946382	0.85[ASN][1000 genomes]
rs61946383	0.82[ASN][1000 genomes]
rs61946384	0.83[ASN][1000 genomes]
rs61946385	0.82[ASN][1000 genomes]
rs61946386	0.82[ASN][1000 genomes]
rs624216	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs625228	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.93[YRI][hapmap];0.85[ASN][1000 genomes]
rs647881	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489780	0.86[YRI][hapmap]
rs6489782	0.82[YRI][hapmap]
rs661647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs665585	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs666976	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7135147	0.86[YRI][hapmap]
rs7137504	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs7139145	0.86[YRI][hapmap]
rs715319	0.86[YRI][hapmap]
rs7298639	0.86[YRI][hapmap]
rs73413868	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73415720	0.85[ASN][1000 genomes]
rs73415734	0.82[ASN][1000 genomes]
rs7965332	0.86[YRI][hapmap]
rs7969140	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7980311	0.85[ASN][1000 genomes]
rs869781	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs909053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9431	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs989986	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs989987	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs610694	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs610694	P2RX4	cis	cerebellum	SCAN
rs610694	SPPL3	cis	cerebellum	SCAN
rs610694	UNQ1887	cis	Temporal Cortex	GTEx
rs610694	HPD	cis	parietal	SCAN
rs610694	WSB2	cis	cerebellum	SCAN
rs610694	SPPL3	cis	parietal	SCAN
rs610694	RPLP0	cis	Skin Sun Exposed Lower leg	GTEx
rs610694	SRRM4	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121282000-121308600	Weak transcription	Fetal Kidney	kidney
2	chr12:121283200-121310200	Weak transcription	Placenta	Placenta
3	chr12:121283400-121307400	Weak transcription	Esophagus	oesophagus
4	chr12:121288000-121311800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:121288000-121316600	Weak transcription	NHLF	lung
6	chr12:121288200-121339600	Weak transcription	Hela-S3	cervix
7	chr12:121291600-121312400	Weak transcription	Gastric	stomach
8	chr12:121292000-121312400	Weak transcription	Aorta	Aorta
9	chr12:121292400-121305600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:121293000-121308200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr12:121294200-121340400	Weak transcription	HSMM	muscle
12	chr12:121294600-121310200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:121295000-121310200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:121295000-121310200	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:121295000-121311000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:121295000-121316200	Weak transcription	HMEC	breast
17	chr12:121295600-121305200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:121295800-121307600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:121296200-121311000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:121296600-121310800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:121296800-121309800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:121297200-121305200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:121297200-121309200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr12:121297200-121310200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:121297400-121305600	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:121297400-121311800	Weak transcription	Dnd41	blood
27	chr12:121297400-121339800	Weak transcription	A549	lung
28	chr12:121297600-121315200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:121298000-121305200	Weak transcription	Fetal Intestine Small	intestine
30	chr12:121298200-121305200	Weak transcription	Fetal Stomach	stomach
31	chr12:121298200-121307600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr12:121298400-121313600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:121299800-121307600	Weak transcription	NHEK	skin
34	chr12:121300200-121305600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:121300600-121305200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:121300600-121310000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:121300600-121310200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr12:121300600-121310200	Weak transcription	Psoas Muscle	Psoas
39	chr12:121300600-121310400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:121300600-121312400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr12:121300600-121328800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:121300800-121309400	Weak transcription	Brain Hippocampus Middle	brain
43	chr12:121301600-121305200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:121302000-121328800	Weak transcription	Fetal Intestine Large	intestine
45	chr12:121303200-121305200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:121303200-121310200	Weak transcription	Adipose Nuclei	Adipose
47	chr12:121303200-121310200	Weak transcription	Brain Anterior Caudate	brain
48	chr12:121303200-121310200	Weak transcription	Right Atrium	heart
49	chr12:121303400-121308200	Weak transcription	Brain Substantia Nigra	brain
50	chr12:121303400-121309600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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