Variant report

Variant	rs838561
Chromosome Location	chr2:234398417-234398418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr2:234398226-234398730	SK-N-SH	brain:	n/a	n/a
2	FOS	chr2:234398362-234398761	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr2:234398387-234398761	Hela-S3	cervix:	n/a	chr2:234398572-234398585
4	GATA3	chr2:234397959-234398804	SK-N-SH	brain:	n/a	n/a
5	FOS	chr2:234398362-234398723	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr2:234398358-234398787	IMR90	lung:	n/a	chr2:234398572-234398585
7	FOS	chr2:234398384-234398722	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr2:234398403-234398567	Hela-S3	cervix:	n/a	n/a
9	GATA3	chr2:234397926-234398911	SK-N-SH	brain:	n/a	n/a
10	FOS	chr2:234398407-234398731	MCF10A-Er-Src	breast:	n/a	n/a
11	E2F4	chr2:234398364-234398678	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234388753..234400184-chr2:234596527..234603213,35	MCF-7	breast:
2	chr2:234386983..234399433-chr2:234613282..234621553,23	MCF-7	breast:
3	chr2:234393753..234400835-chr2:234472864..234476478,8	MCF-7	breast:
4	chr2:234393680..234401613-chr2:234597738..234605139,18	MCF-7	breast:

Variant related genes	Relation type
USP40	TF binding region
ENSG00000167165	Chromatin interaction
ENSG00000085982	Chromatin interaction
ENSG00000224814	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10168794	1.00[JPT][hapmap]
rs10169180	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10177112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10178062	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10178357	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10183033	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10185923	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10193542	1.00[JPT][hapmap]
rs10198879	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10199833	1.00[CHB][hapmap]
rs10207915	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10208361	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1037451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10803653	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10929195	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10929200	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10929208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1097929	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1097930	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1097931	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11690686	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11892545	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1220430	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12467878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12473743	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12473824	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12615446	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12692193	0.93[EUR][1000 genomes]
rs12692195	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13002253	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13018364	0.91[EUR][1000 genomes]
rs13384932	1.00[JPT][hapmap]
rs13400563	1.00[JPT][hapmap]
rs13427703	1.00[CHB][hapmap]
rs1377459	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1377461	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1453321	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1470864	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1470865	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1542325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1542326	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1545525	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1597940	1.00[CEU][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1901812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2034675	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2124045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167884	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2167885	1.00[CEU][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2602387	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2602389	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2603545	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2603546	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2603547	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2924809	1.00[JPT][hapmap];0.98[EUR][1000 genomes]
rs2924810	0.82[EUR][1000 genomes]
rs2924811	0.95[EUR][1000 genomes]
rs2924813	0.93[EUR][1000 genomes]
rs2971861	0.98[EUR][1000 genomes]
rs2971862	0.99[EUR][1000 genomes]
rs2971863	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2971864	1.00[EUR][1000 genomes]
rs2971865	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs2971866	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2971867	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2971869	0.91[EUR][1000 genomes]
rs2971870	0.95[EUR][1000 genomes]
rs2971871	0.95[EUR][1000 genomes]
rs2971872	0.95[EUR][1000 genomes]
rs2971873	0.80[EUR][1000 genomes]
rs3792104	1.00[CHB][hapmap]
rs3792105	1.00[CHB][hapmap]
rs4047187	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4047188	0.92[EUR][1000 genomes]
rs4047198	1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4047199	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4233627	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4663684	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4663698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55679565	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59160392	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710645	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6710772	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6716988	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6720619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6726184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6753062	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6756068	1.00[CEU][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7422734	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7557849	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7567713	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7571288	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7572310	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7575694	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7578898	1.00[CEU][hapmap];0.94[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7588509	1.00[CHB][hapmap]
rs7599285	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7603410	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7604337	0.86[EUR][1000 genomes]
rs7724	0.98[EUR][1000 genomes]
rs838543	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs838544	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs838545	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs838548	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs838549	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs838550	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs838551	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs838552	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs838555	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs838557	0.94[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs838558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838559	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs838562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860794	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs896833	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv1000870	chr2:234333083-234410768	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv3214	chr2:234384436-234416949	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234343000-234402200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:234364000-234411200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:234373000-234409800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:234373800-234404400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:234375400-234411200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:234381600-234399600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr2:234383400-234400200	Strong transcription	Fetal Intestine Small	intestine
8	chr2:234384000-234412400	Weak transcription	Fetal Heart	heart
9	chr2:234384400-234402200	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr2:234384400-234402600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:234384600-234408400	Strong transcription	Duodenum Mucosa	Duodenum
12	chr2:234386600-234400800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:234386800-234407800	Strong transcription	Fetal Intestine Large	intestine
14	chr2:234387400-234402800	Strong transcription	Adipose Nuclei	Adipose
15	chr2:234387400-234466000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:234388200-234402000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:234388400-234401800	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr2:234390200-234402800	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr2:234390800-234441000	Weak transcription	Fetal Brain Male	brain
20	chr2:234391200-234404400	Strong transcription	Fetal Stomach	stomach
21	chr2:234391400-234402600	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:234391600-234412000	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:234392000-234411600	Weak transcription	Fetal Brain Female	brain
24	chr2:234392200-234402400	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:234392400-234399400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:234392400-234403000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:234392800-234406400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:234393000-234400800	Weak transcription	GM12878-XiMat	blood
29	chr2:234393000-234402400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:234393600-234401000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr2:234393800-234403200	Strong transcription	Primary T cells from cord blood	blood
32	chr2:234394000-234403200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:234394200-234402600	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:234394400-234399200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr2:234394400-234399600	Genic enhancers	NHEK	skin
36	chr2:234394400-234401000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:234394800-234398800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:234395200-234399200	Enhancers	HMEC	breast
39	chr2:234395200-234399600	Weak transcription	Dnd41	blood
40	chr2:234395200-234406000	Weak transcription	Fetal Kidney	kidney
41	chr2:234395400-234404200	Weak transcription	Stomach Mucosa	stomach
42	chr2:234395600-234402200	Strong transcription	Left Ventricle	heart
43	chr2:234395600-234402600	Strong transcription	Right Ventricle	heart
44	chr2:234395600-234404800	Strong transcription	Fetal Muscle Trunk	muscle
45	chr2:234395600-234431800	Weak transcription	Colonic Mucosa	Colon
46	chr2:234395800-234399600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:234395800-234401600	Weak transcription	Aorta	Aorta
48	chr2:234395800-234402000	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr2:234395800-234408000	Strong transcription	Fetal Muscle Leg	muscle
50	chr2:234395800-234411400	Strong transcription	Liver	Liver

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