Variant report

Variant	rs3769995
Chromosome Location	chr2:178348620-178348621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178300117..178301731-chr2:178348147..178350153,2	K562	blood:
2	chr2:178336406..178340265-chr2:178346477..178351406,5	K562	blood:
3	chr2:178336406..178338882-chr2:178346745..178351095,3	K562	blood:
4	chr2:178341565..178343959-chr2:178347288..178350087,2	K562	blood:

Variant related genes	Relation type
ENSG00000018510	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10165785	0.86[ASN][1000 genomes]
rs10170546	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10170667	0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs10176632	0.82[ASN][1000 genomes]
rs10194648	0.89[ASN][1000 genomes]
rs10201153	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10497502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10497503	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10497508	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10803909	0.83[ASN][1000 genomes]
rs10930792	0.87[ASN][1000 genomes]
rs11688684	0.81[JPT][hapmap]
rs11893448	0.85[ASN][1000 genomes]
rs12104588	0.81[ASN][1000 genomes]
rs12469386	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12611938	0.81[ASN][1000 genomes]
rs12614820	0.81[ASN][1000 genomes]
rs12615367	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs12616093	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs12616443	0.85[ASN][1000 genomes]
rs12618139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619453	1.00[YRI][hapmap]
rs12620035	0.86[ASN][1000 genomes]
rs12693120	0.85[ASN][1000 genomes]
rs12990729	0.86[ASN][1000 genomes]
rs12996447	0.82[ASN][1000 genomes]
rs13000048	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs13004955	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs13027959	0.82[ASN][1000 genomes]
rs1348848	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1348849	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1348850	0.85[JPT][hapmap]
rs1374437	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1453370	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1453371	0.82[ASN][1000 genomes]
rs1453373	0.91[JPT][hapmap]
rs16865203	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16865216	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16865229	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16865291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16865328	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs16865331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1901825	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs1901826	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1979058	0.87[ASN][1000 genomes]
rs2034678	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2060929	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2084233	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2121430	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2166558	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2197611	0.89[ASN][1000 genomes]
rs2364853	0.98[ASN][1000 genomes]
rs2364854	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3213945	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs3769996	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770002	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3813259	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3902850	0.87[ASN][1000 genomes]
rs4243388	0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4341974	0.85[ASN][1000 genomes]
rs4893821	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs4893822	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4893823	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4893824	0.86[ASN][1000 genomes]
rs4893825	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4893935	0.95[JPT][hapmap]
rs4893936	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs4893938	0.81[ASN][1000 genomes]
rs4893941	0.85[ASN][1000 genomes]
rs4893944	0.82[ASN][1000 genomes]
rs4893945	0.85[ASN][1000 genomes]
rs4893946	0.81[ASN][1000 genomes]
rs4893950	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4893951	0.95[ASN][1000 genomes]
rs4893954	0.86[ASN][1000 genomes]
rs4893957	0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs4893959	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs4893961	0.86[JPT][hapmap]
rs4893962	0.86[JPT][hapmap]
rs56942680	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57273542	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57295810	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57527255	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57541536	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57733896	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57948641	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58297927	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58483300	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59111239	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59421055	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59504156	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59578457	0.81[ASN][1000 genomes]
rs59751564	0.84[ASN][1000 genomes]
rs60642012	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs60670838	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60733259	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6433670	0.89[ASN][1000 genomes]
rs6433673	0.86[ASN][1000 genomes]
rs6710575	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs6742951	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7565022	0.85[ASN][1000 genomes]
rs7573763	0.81[ASN][1000 genomes]
rs7586051	0.85[ASN][1000 genomes]
rs7587604	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7591807	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7604673	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7606235	0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7607450	0.89[ASN][1000 genomes]
rs8941	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs952746	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9679607	0.87[ASN][1000 genomes]
rs9789582	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178296400-178397000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr2:178298800-178357800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:178299400-178357800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:178330800-178356800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:178331000-178354600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:178331000-178357800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:178331000-178357800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:178331000-178361600	Weak transcription	Brain Substantia Nigra	brain
9	chr2:178331000-178378600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:178331200-178349000	Weak transcription	Left Ventricle	heart
11	chr2:178331200-178355000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:178331200-178358000	Weak transcription	Brain Angular Gyrus	brain
13	chr2:178331200-178378600	Weak transcription	Placenta	Placenta
14	chr2:178331200-178379200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:178331400-178388400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr2:178331600-178351800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:178331600-178357800	Weak transcription	Colonic Mucosa	Colon
18	chr2:178331600-178385600	Weak transcription	Spleen	Spleen
19	chr2:178331800-178349800	Weak transcription	Esophagus	oesophagus
20	chr2:178331800-178351200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:178331800-178360600	Weak transcription	Lung	lung
22	chr2:178331800-178373800	Weak transcription	Gastric	stomach
23	chr2:178331800-178375800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:178331800-178375800	Weak transcription	Pancreas	Pancrea
25	chr2:178331800-178389400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:178332000-178392800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:178332000-178393800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:178332800-178356800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:178335000-178410600	Weak transcription	Thymus	Thymus
30	chr2:178335200-178349000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:178337400-178356800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:178337400-178357800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:178337400-178358000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr2:178337600-178386200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:178337800-178352400	Weak transcription	Psoas Muscle	Psoas
36	chr2:178338000-178403000	Weak transcription	Brain Hippocampus Middle	brain
37	chr2:178338200-178357800	Weak transcription	Fetal Intestine Large	intestine
38	chr2:178339000-178359800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:178339200-178349000	Weak transcription	Fetal Stomach	stomach
40	chr2:178339400-178349000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:178339400-178349000	Weak transcription	Ovary	ovary
42	chr2:178339400-178351000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:178339400-178357800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:178339800-178394400	Weak transcription	Hela-S3	cervix
45	chr2:178340200-178358000	Weak transcription	Aorta	Aorta
46	chr2:178340200-178358000	Weak transcription	HSMMtube	muscle
47	chr2:178341800-178354400	Weak transcription	Fetal Kidney	kidney
48	chr2:178342400-178357800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:178342400-178392000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:178342600-178349000	Weak transcription	Osteobl	bone

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