Variant report

Variant	rs3902850
Chromosome Location	chr2:178315899-178315900
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	chr2:178315080..178317841-chr2:178326104..178328260,2	K562	blood:
2	chr2:178308571..178311721-chr2:178313471..178317393,4	K562	blood:

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10165785	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10170546	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10170667	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10171135	0.86[YRI][hapmap]
rs10194648	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10208150	0.80[ASN][1000 genomes]
rs10497501	0.90[CEU][hapmap]
rs10497502	0.86[ASN][1000 genomes]
rs10497503	1.00[CEU][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10497508	0.86[ASN][1000 genomes]
rs10803909	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10930792	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11889272	0.93[YRI][hapmap]
rs11893448	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12104588	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12469386	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12612857	0.89[CEU][hapmap]
rs12615367	0.80[ASN][1000 genomes]
rs12616093	0.80[ASN][1000 genomes]
rs12616443	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12618139	0.87[ASN][1000 genomes]
rs12693120	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12990729	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12996447	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13000048	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13004955	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13020788	0.80[CEU][hapmap]
rs13027959	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1348848	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1348849	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1348850	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1374437	1.00[CEU][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1405713	0.90[CEU][hapmap]
rs1453370	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1548067	0.89[CEU][hapmap]
rs16865203	0.86[ASN][1000 genomes]
rs16865216	0.86[ASN][1000 genomes]
rs16865229	0.86[ASN][1000 genomes]
rs16865291	0.87[ASN][1000 genomes]
rs16865331	0.81[ASN][1000 genomes]
rs1901824	0.85[ASN][1000 genomes]
rs1901825	0.85[ASN][1000 genomes]
rs1901826	0.84[YRI][hapmap]
rs1901829	0.86[ASN][1000 genomes]
rs1979058	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2060929	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2084233	1.00[CEU][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2121430	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2166558	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2197611	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364845	0.85[ASN][1000 genomes]
rs2364853	0.85[ASN][1000 genomes]
rs2364854	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3213945	0.81[ASN][1000 genomes]
rs3769995	0.87[ASN][1000 genomes]
rs3769996	0.87[ASN][1000 genomes]
rs3769997	0.87[ASN][1000 genomes]
rs3770002	0.89[ASN][1000 genomes]
rs3813259	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4243388	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4341974	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4528793	0.90[CEU][hapmap]
rs4893821	0.85[ASN][1000 genomes]
rs4893822	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4893823	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4893824	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4893825	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4893931	0.80[ASN][1000 genomes]
rs4893932	0.84[ASN][1000 genomes]
rs4893934	0.85[ASN][1000 genomes]
rs4893935	0.83[ASN][1000 genomes]
rs4893936	0.86[ASN][1000 genomes]
rs4893938	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4893941	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4893944	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4893945	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4893946	0.93[ASN][1000 genomes]
rs4893950	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4893951	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4893954	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4893957	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4893959	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4893961	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4893962	0.90[CEU][hapmap]
rs4893965	0.89[CEU][hapmap]
rs56942680	0.82[ASN][1000 genomes]
rs57273542	0.86[ASN][1000 genomes]
rs57295810	0.87[ASN][1000 genomes]
rs57527255	0.89[ASN][1000 genomes]
rs57541536	0.89[ASN][1000 genomes]
rs57733896	0.86[ASN][1000 genomes]
rs57948641	0.89[ASN][1000 genomes]
rs58297927	0.89[ASN][1000 genomes]
rs58483300	0.82[ASN][1000 genomes]
rs59111239	0.86[ASN][1000 genomes]
rs59421055	0.84[ASN][1000 genomes]
rs59504156	0.87[ASN][1000 genomes]
rs60642012	0.84[ASN][1000 genomes]
rs60670838	0.86[ASN][1000 genomes]
rs60733259	0.82[ASN][1000 genomes]
rs6433670	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6433673	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6710575	1.00[CEU][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6737342	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs6742951	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6752528	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs7565022	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7573763	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7586051	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7587604	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7591807	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7604673	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7606235	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7607450	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8941	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs952746	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9679607	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9789582	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3902850	DKFZp451M2119	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178295400-178329800	Weak transcription	Pancreas	Pancrea
2	chr2:178295400-178330000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:178295400-178330200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:178296400-178397000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr2:178296600-178319800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:178297800-178319600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:178297800-178329800	Weak transcription	Ovary	ovary
8	chr2:178298800-178329200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:178298800-178329800	Weak transcription	Colonic Mucosa	Colon
10	chr2:178298800-178329800	Weak transcription	Thymus	Thymus
11	chr2:178298800-178330200	Weak transcription	Aorta	Aorta
12	chr2:178298800-178330200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:178298800-178331600	Weak transcription	NHDF-Ad	bronchial
14	chr2:178298800-178336800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:178298800-178357800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:178299000-178329800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:178299000-178330200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:178299400-178357800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:178300800-178331400	Weak transcription	Psoas Muscle	Psoas
20	chr2:178301000-178330200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:178301600-178339800	Weak transcription	Small Intestine	intestine
22	chr2:178301800-178339200	Weak transcription	Hela-S3	cervix
23	chr2:178302200-178329400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:178304200-178316600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:178304400-178338800	Weak transcription	HMEC	breast
26	chr2:178304800-178316200	Weak transcription	Colon Smooth Muscle	Colon
27	chr2:178305200-178329800	Weak transcription	Esophagus	oesophagus
28	chr2:178305600-178330000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:178305800-178329400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:178305800-178330200	Weak transcription	Brain Substantia Nigra	brain
31	chr2:178306000-178331200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:178306600-178330400	Weak transcription	Brain Angular Gyrus	brain
33	chr2:178307000-178316400	Weak transcription	Brain Anterior Caudate	brain
34	chr2:178307200-178330200	Weak transcription	NHEK	skin
35	chr2:178307600-178319800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:178307800-178330600	Weak transcription	Osteobl	bone
37	chr2:178308800-178329400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:178309200-178329800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr2:178310200-178316000	Weak transcription	Right Ventricle	heart
40	chr2:178310200-178320600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:178310800-178319600	Weak transcription	HUVEC	blood vessel
42	chr2:178310800-178330200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:178311200-178330200	Weak transcription	Lung	lung
44	chr2:178312200-178321600	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr2:178312600-178317000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:178313000-178330400	Weak transcription	Right Atrium	heart
47	chr2:178313400-178330200	Weak transcription	HSMMtube	muscle
48	chr2:178313800-178331400	Weak transcription	NH-A	brain
49	chr2:178314000-178319400	Weak transcription	K562	blood
50	chr2:178314000-178319600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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