Variant report

Variant	rs11682044
Chromosome Location	chr2:48540744-48540745
allele	A/C
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	SMC3	chr2:48540684-48542019	GM12878	blood:	n/a	chr2:48541837-48541845
2	RCOR1	chr2:48540730-48543576	GM12878	blood:	n/a	n/a
3	ATF2	chr2:48540729-48541627	GM12878	blood:	n/a	n/a
4	NFIC	chr2:48540637-48541758	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:48540107-48543489	GM12891	blood:	n/a	n/a
6	POLR2A	chr2:48540301-48543417	GM18951	blood:	n/a	n/a
7	RELA	chr2:48540295-48543281	GM15510	blood:	n/a	n/a
8	POLR2A	chr2:48540308-48543338	K562	blood:	n/a	n/a
9	POLR2A	chr2:48540282-48543461	Raji	blood:	n/a	n/a
10	TBL1XR1	chr2:48540725-48542358	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:48540239-48543382	GM12892	blood:	n/a	n/a
12	POLR2A	chr2:48540673-48543277	PBDE	blood:	n/a	n/a
13	CTCF	chr2:48540661-48543738	A549	lung:	n/a	chr2:48541659-48541672 chr2:48542391-48542404 chr2:48541998-48542011
14	FOXM1	chr2:48540614-48542004	GM12878	blood:	n/a	n/a
15	POLR2A	chr2:48540505-48540966	HepG2	liver:	n/a	n/a
16	POLR2A	chr2:48540171-48543452	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:48540139-48543407	GM15510	blood:	n/a	n/a
18	RELA	chr2:48540241-48543316	GM19099	blood:	n/a	n/a
19	RELA	chr2:48540408-48542364	GM10847	blood:	n/a	n/a
20	GATA3	chr2:48540691-48540914	SH-SY5Y	brain:	n/a	n/a
21	TBP	chr2:48540285-48543395	K562	blood:	n/a	n/a
22	KAP1	chr2:48540528-48540889	K562	blood:	n/a	n/a
23	BATF	chr2:48540708-48541073	GM12878	blood:	n/a	n/a
24	MTA3	chr2:48540517-48541521	GM12878	blood:	n/a	n/a
25	POLR2A	chr2:48540517-48540942	GM12892	blood:	n/a	n/a
26	RUNX3	chr2:48540550-48543464	GM12878	blood:	n/a	n/a
27	MXI1	chr2:48540626-48540822	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:48540697-48540866	HepG2	liver:	n/a	n/a
29	CHD1	chr2:48540591-48541575	GM12878	blood:	n/a	n/a
30	NFIC	chr2:48540455-48541737	GM12878	blood:	n/a	n/a
31	MTA3	chr2:48540374-48543565	GM12878	blood:	n/a	n/a
32	POLR2A	chr2:48540733-48541484	HCT-116	colon:	n/a	n/a
33	CREB1	chr2:48540583-48543392	GM12878	blood:	n/a	n/a
34	POLR2A	chr2:48540232-48543419	GM18505	blood:	n/a	n/a
35	GATA1	chr2:48540572-48542359	PBDE	blood:	n/a	n/a
36	HEY1	chr2:48540113-48543427	HepG2	liver:	n/a	chr2:48542008-48542023 chr2:48542497-48542512 chr2:48541386-48541401
37	POLR2A	chr2:48540589-48540892	GM12891	blood:	n/a	n/a
38	TBP	chr2:48540714-48541996	GM12878	blood:	n/a	n/a
39	POLR2A	chr2:48540407-48543317	K562	blood:	n/a	n/a
40	POLR2A	chr2:48540299-48543355	GM12878	blood:	n/a	n/a
41	E2F4	chr2:48540441-48542075	MCF10A-Er-Src	breast:	n/a	chr2:48541425-48541434 chr2:48541481-48541488 chr2:48541395-48541404 chr2:48541481-48541488 chr2:48541649-48541664 chr2:48541964-48541973 chr2:48541387-48541396 chr2:48541481-48541488 chr2:48541648-48541660 chr2:48541477-48541491 chr2:48541479-48541490
42	JUN	chr2:48539938-48543624	K562	blood:	n/a	chr2:48540933-48540945 chr2:48541697-48541706
43	POLR2A	chr2:48540208-48543378	GM19193	blood:	n/a	n/a
44	RELA	chr2:48540652-48543415	GM18951	blood:	n/a	n/a
45	POLR2A	chr2:48540354-48543368	K562	blood:	n/a	n/a
46	POLR2A	chr2:48540521-48543391	HepG2	liver:	n/a	n/a
47	ATF2	chr2:48540569-48542082	GM12878	blood:	n/a	n/a
48	PML	chr2:48540420-48543610	GM12878	blood:	n/a	chr2:48543213-48543221
49	EP300	chr2:48540359-48543447	GM12878	blood:	n/a	chr2:48542120-48542129 chr2:48541995-48542011 chr2:48540955-48540965 chr2:48541989-48542005 chr2:48542013-48542029 chr2:48542020-48542036 chr2:48541827-48541843 chr2:48542646-48542655
50	NFATC1	chr2:48540533-48541741	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:48539557..48542081-chr2:48666297..48668955,4	MCF-7	breast:
2	chr2:48499034..48501158-chr2:48538819..48540781,2	K562	blood:
3	chr2:48515255..48518583-chr2:48539283..48541492,3	K562	blood:
4	chr2:48492280..48493854-chr2:48539785..48541732,2	K562	blood:
5	chr2:48532704..48536258-chr2:48538581..48541257,5	K562	blood:
6	chr2:48540677..48543829-chr2:48665802..48669252,3	K562	blood:

Variant related genes	Relation type
FOXN2	TF binding region
ENSG00000272663	Chromatin interaction
ENSG00000162869	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10153773	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10174717	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180295	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10186237	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10193072	0.98[ASN][1000 genomes]
rs10199431	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10208124	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10454133	0.95[MEX][hapmap]
rs10495951	0.83[JPT][hapmap]
rs10495952	0.83[JPT][hapmap]
rs11676168	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11679523	0.83[JPT][hapmap]
rs11680916	0.86[JPT][hapmap]
rs11682931	0.84[EUR][1000 genomes]
rs11685861	0.88[ASW][hapmap];0.85[CEU][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11688481	0.83[JPT][hapmap]
rs11690690	0.83[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11690748	0.83[JPT][hapmap]
rs11690845	0.83[JPT][hapmap]
rs12616792	0.87[ASN][1000 genomes]
rs12713008	0.87[ASN][1000 genomes]
rs12713009	0.87[ASN][1000 genomes]
rs13383364	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13385535	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13386751	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13387171	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13388291	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13392004	0.81[EUR][1000 genomes]
rs13426834	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13432998	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17037289	0.83[JPT][hapmap]
rs17037298	0.83[JPT][hapmap]
rs17855177	0.83[JPT][hapmap]
rs2471405	0.85[ASN][1000 genomes]
rs28806843	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28841370	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4290706	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4344965	0.85[CEU][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs4411759	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4547573	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4641990	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.90[ASN][1000 genomes]
rs56352447	0.94[ASN][1000 genomes]
rs57668696	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58660534	0.89[ASN][1000 genomes]
rs59264464	0.90[ASN][1000 genomes]
rs59412192	0.90[ASN][1000 genomes]
rs59761994	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60677957	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62136987	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62137001	0.89[ASN][1000 genomes]
rs62137002	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62137003	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62137005	0.89[ASN][1000 genomes]
rs62137006	0.89[ASN][1000 genomes]
rs62137007	0.89[ASN][1000 genomes]
rs62137008	0.87[ASN][1000 genomes]
rs62137009	0.87[ASN][1000 genomes]
rs62137015	0.84[EUR][1000 genomes]
rs62138801	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545026	0.92[YRI][hapmap]
rs6545027	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545028	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545029	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545030	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545034	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545035	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545036	0.84[CEU][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6705802	0.83[JPT][hapmap];0.88[YRI][hapmap]
rs6712029	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6718068	0.83[JPT][hapmap]
rs6743757	0.84[CEU][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs6757206	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72818493	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72820405	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72887649	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7340322	0.88[ASN][1000 genomes]
rs7562069	0.85[CEU][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs7562816	0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs7566239	0.83[JPT][hapmap];0.96[YRI][hapmap]
rs7568960	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7574125	0.83[ASN][1000 genomes]
rs7576964	0.87[JPT][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap]
rs7577237	0.83[JPT][hapmap];0.96[YRI][hapmap]
rs7579932	0.88[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7600794	0.85[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7606104	0.88[ASW][hapmap];0.85[CEU][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9309152	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription 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 miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48538600-48540800	Enhancers	Fetal Intestine Large	intestine
2	chr2:48538800-48541200	Enhancers	NHEK	skin
3	chr2:48539000-48541000	Enhancers	Fetal Intestine Small	intestine
4	chr2:48539200-48541000	Enhancers	HMEC	breast
5	chr2:48539400-48541000	Weak transcription	Stomach Mucosa	stomach
6	chr2:48539600-48540800	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr2:48539600-48541000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:48539800-48540800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:48539800-48541000	Weak transcription	Hela-S3	cervix
10	chr2:48540200-48540800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:48540200-48540800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr2:48540200-48540800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
13	chr2:48540200-48540800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:48540200-48540800	Enhancers	Fetal Muscle Leg	muscle
15	chr2:48540200-48540800	Enhancers	Placenta	Placenta
16	chr2:48540200-48540800	Enhancers	Fetal Thymus	thymus
17	chr2:48540200-48540800	Enhancers	NHDF-Ad	bronchial
18	chr2:48540200-48541000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:48540200-48541000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr2:48540200-48541000	Enhancers	Colonic Mucosa	Colon
21	chr2:48540200-48541000	Enhancers	Fetal Heart	heart
22	chr2:48540200-48541000	Enhancers	Pancreas	Pancrea
23	chr2:48540200-48541000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr2:48540200-48541000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr2:48540200-48541200	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr2:48540200-48541400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr2:48540200-48541400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr2:48540200-48541400	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr2:48540200-48541400	Flanking Active TSS	Dnd41	blood
30	chr2:48540200-48541400	Flanking Active TSS	K562	blood
31	chr2:48540200-48542800	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr2:48540200-48543000	Active TSS	Thymus	Thymus
33	chr2:48540400-48540800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr2:48540400-48540800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:48540400-48540800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr2:48540400-48540800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:48540400-48540800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:48540400-48540800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:48540400-48540800	Enhancers	Liver	Liver
40	chr2:48540400-48540800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr2:48540400-48540800	Enhancers	HUVEC	blood vessel
42	chr2:48540400-48541000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr2:48540400-48541000	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr2:48540400-48541000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:48540400-48541000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr2:48540400-48541200	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr2:48540400-48541200	Flanking Active TSS	HepG2	liver
48	chr2:48540400-48541400	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr2:48540400-48541800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:48540400-48541800	Weak transcription	Small Intestine	intestine

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