Variant report

Variant	rs6540553
Chromosome Location	chr1:209929044-209929045
allele	C/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	RCOR1	chr1:209928960-209930409	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:209928692-209932543	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:209929004-209931083	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:209928989-209931083	GM12892	blood:	n/a	n/a
5	RELA	chr1:209928787-209930749	GM19099	blood:	n/a	chr1:209928807-209928816 chr1:209928807-209928816
6	POLR2A	chr1:209929032-209933590	GM12878	blood:	n/a	n/a
7	RUNX3	chr1:209928960-209930858	GM12878	blood:	n/a	chr1:209929212-209929221 chr1:209929212-209929221
8	RUNX3	chr1:209928948-209930753	GM12878	blood:	n/a	chr1:209929212-209929221 chr1:209929212-209929221
9	TBL1XR1	chr1:209929010-209930486	GM12878	blood:	n/a	n/a
10	TBP	chr1:209929015-209930614	GM12878	blood:	n/a	n/a
11	RELA	chr1:209928660-209930846	GM18951	blood:	n/a	chr1:209928807-209928816 chr1:209928807-209928816
12	MAX	chr1:209928994-209930579	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:209929034-209930872	GM18526	blood:	n/a	n/a
14	IKZF1	chr1:209928708-209930301	GM12878	blood:	n/a	chr1:209929687-209929699 chr1:209928803-209928815
15	SPI1	chr1:209928921-209929890	GM12878	blood:	n/a	chr1:209929416-209929429
16	MTA3	chr1:209929043-209930489	GM12878	blood:	n/a	n/a
17	NFIC	chr1:209928871-209930425	GM12878	blood:	n/a	n/a
18	MTA3	chr1:209928980-209930787	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
TRAF3IP3	TF binding region

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1000282	0.84[EUR][1000 genomes]
rs1000283	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs1007693	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10157973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489342	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10863783	0.85[EUR][1000 genomes]
rs10863785	0.85[EUR][1000 genomes]
rs11119327	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs11119330	0.85[EUR][1000 genomes]
rs11119331	0.85[EUR][1000 genomes]
rs11119332	0.84[EUR][1000 genomes]
rs11119336	1.00[CEU][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11119338	0.89[JPT][hapmap]
rs11119340	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs11119341	0.80[CEU][hapmap];0.89[JPT][hapmap]
rs11485195	0.85[EUR][1000 genomes]
rs11487866	0.85[EUR][1000 genomes]
rs11487867	0.86[CEU][hapmap]
rs11808690	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs12030655	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12034758	0.95[CEU][hapmap];0.80[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12059226	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs12060420	0.85[EUR][1000 genomes]
rs12060922	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs12086634	0.85[EUR][1000 genomes]
rs12090931	0.85[EUR][1000 genomes]
rs12094117	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs12116437	0.85[EUR][1000 genomes]
rs12120361	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs12138452	0.85[EUR][1000 genomes]
rs1415542	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs17389184	0.85[CEU][hapmap]
rs17389198	1.00[CEU][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1999826	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076150	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2236903	0.90[CEU][hapmap]
rs2272867	1.00[CEU][hapmap];0.89[JPT][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2282738	0.85[CEU][hapmap]
rs2282739	0.90[CEU][hapmap]
rs3765240	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766618	0.85[CEU][hapmap]
rs3766619	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs3817821	0.83[EUR][1000 genomes]
rs4844891	0.90[CEU][hapmap]
rs627670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs643118	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6540549	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs6540550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540551	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540552	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540554	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6540555	0.86[ASN][1000 genomes]
rs6540556	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6665715	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6672256	0.85[EUR][1000 genomes]
rs667681	0.85[EUR][1000 genomes]
rs6679099	0.85[EUR][1000 genomes]
rs6679405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679631	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6685077	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6691905	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6696463	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6702301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752	0.85[EUR][1000 genomes]
rs679846	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521461	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532324	0.82[EUR][1000 genomes]
rs7536882	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7539852	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs7548219	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7548781	0.90[CEU][hapmap]
rs909710	1.00[CEU][hapmap];0.89[JPT][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs932335	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs9430012	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs9430014	0.85[EUR][1000 genomes]
rs9430016	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9430017	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.86[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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1001588	chr1:209908876-209938243	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209921400-209929800	Weak transcription	Right Atrium	heart
2	chr1:209921400-209930000	Weak transcription	Right Ventricle	heart
3	chr1:209921800-209929600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:209921800-209930000	Weak transcription	Stomach Mucosa	stomach
5	chr1:209921800-209940800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:209921800-209942000	Weak transcription	Pancreas	Pancrea
7	chr1:209922400-209931200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:209926000-209929600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:209927800-209929200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:209927800-209929400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr1:209928200-209929200	Enhancers	Primary B cells from peripheral blood	blood
12	chr1:209928400-209929400	Enhancers	Primary hematopoietic stem cells	blood
13	chr1:209928400-209929400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr1:209928600-209929200	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr1:209928600-209929400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr1:209928600-209929400	Enhancers	Fetal Intestine Large	intestine
17	chr1:209928600-209929600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:209928600-209932000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr1:209928600-209932200	Flanking Active TSS	GM12878-XiMat	blood
20	chr1:209928800-209929200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:209928800-209929400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:209928800-209929400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr1:209928800-209929400	Enhancers	Fetal Intestine Small	intestine
24	chr1:209928800-209929400	Flanking Active TSS	Fetal Thymus	thymus
25	chr1:209928800-209930400	Flanking Active TSS	Dnd41	blood
26	chr1:209928800-209931000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr1:209928800-209932200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr1:209928800-209932400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr1:209929000-209929200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr1:209929000-209929200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:209929000-209929400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
32	chr1:209929000-209929400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr1:209929000-209929400	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr1:209929000-209929400	Flanking Active TSS	Thymus	Thymus
35	chr1:209929000-209931200	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr1:209929000-209931800	Active TSS	Duodenum Mucosa	Duodenum
37	chr1:209929000-209932000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr1:209929000-209932200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:209929000-209932200	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr1:209929000-209932400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:209929000-209932800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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