Variant report

Variant	rs1007693
Chromosome Location	chr1:209931799-209931800
allele	C/T
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	POLR2A	chr1:209929084-209933092	GM18505	blood:	n/a	n/a
2	POLR2A	chr1:209928692-209932543	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:209929032-209933590	GM12878	blood:	n/a	n/a
4	EBF1	chr1:209931777-209932125	GM12878	blood:	n/a	chr1:209931931-209931942 chr1:209931796-209931806

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209931478..209933302-chr1:209941660..209944063,2	K562	blood:

Variant related genes	Relation type
TRAF3IP3	TF binding region
ENSG00000009790	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1000283	0.81[CEU][hapmap]
rs10157973	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10489342	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863786	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11119327	0.81[CEU][hapmap]
rs11119336	0.85[CEU][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11119337	0.90[EUR][1000 genomes]
rs11119338	0.89[JPT][hapmap]
rs11119340	0.81[CEU][hapmap];0.89[JPT][hapmap]
rs11119341	0.89[JPT][hapmap]
rs12030655	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12034758	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs12059226	0.81[CEU][hapmap]
rs12060922	0.81[CEU][hapmap]
rs12079960	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12094117	0.81[CEU][hapmap]
rs12120361	0.81[CEU][hapmap]
rs1415542	0.81[CEU][hapmap]
rs17015169	0.81[CEU][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17389198	0.86[CEU][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1999826	0.96[ASN][1000 genomes]
rs2076150	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272867	0.85[CEU][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs3753606	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3765240	0.96[ASN][1000 genomes]
rs3766619	0.81[CEU][hapmap]
rs611861	0.86[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs627670	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs643118	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540549	0.81[CEU][hapmap]
rs6540550	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6540551	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6540552	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6540553	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6540554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540555	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6540556	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs654984	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6665715	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679405	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6679631	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6685077	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691905	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6696463	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700223	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6702301	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs679846	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7521461	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7536882	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7539852	0.81[CEU][hapmap]
rs7548219	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs909710	0.85[CEU][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs932335	0.81[CEU][hapmap]
rs9430012	0.81[CEU][hapmap]
rs9430016	0.81[CEU][hapmap]
rs9430017	0.86[CEU][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209921800-209940800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209921800-209942000	Weak transcription	Pancreas	Pancrea
3	chr1:209928600-209932000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr1:209928600-209932200	Flanking Active TSS	GM12878-XiMat	blood
5	chr1:209928800-209932200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr1:209928800-209932400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr1:209929000-209931800	Active TSS	Duodenum Mucosa	Duodenum
8	chr1:209929000-209932000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr1:209929000-209932200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:209929000-209932200	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr1:209929000-209932400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:209929000-209932800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:209929400-209931800	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr1:209929400-209931800	Active TSS	Rectal Smooth Muscle	rectum
15	chr1:209930200-209932600	Weak transcription	Right Ventricle	heart
16	chr1:209930200-209934600	Weak transcription	Right Atrium	heart
17	chr1:209930200-209935000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
18	chr1:209930400-209931800	Transcr. at gene 5' and 3'	Dnd41	blood
19	chr1:209930400-209932200	Flanking Active TSS	Thymus	Thymus
20	chr1:209930800-209931800	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr1:209930800-209932200	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
22	chr1:209930800-209932200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:209930800-209932600	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:209930800-209933000	Weak transcription	Fetal Intestine Small	intestine
25	chr1:209930800-209938800	Weak transcription	Fetal Intestine Large	intestine
26	chr1:209931000-209932000	Enhancers	Spleen	Spleen
27	chr1:209931000-209932200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
28	chr1:209931000-209933000	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
29	chr1:209931000-209941800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:209931000-209942000	Weak transcription	Esophagus	oesophagus
31	chr1:209931000-209943200	Weak transcription	Lung	lung
32	chr1:209931000-209943600	Weak transcription	Gastric	stomach
33	chr1:209931200-209931800	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
34	chr1:209931200-209932000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr1:209931200-209932600	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:209931200-209932800	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
37	chr1:209931200-209933400	Enhancers	Fetal Heart	heart
38	chr1:209931200-209933800	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
39	chr1:209931400-209931800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr1:209931400-209932000	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:209931400-209932000	Weak transcription	Colonic Mucosa	Colon
42	chr1:209931400-209932400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr1:209931400-209932800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr1:209931600-209931800	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:209931600-209932000	Enhancers	HSMMtube	muscle
46	chr1:209931600-209932200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:209931600-209932200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:209931600-209933800	Enhancers	Fetal Muscle Leg	muscle

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