Variant report

Variant	rs2272866
Chromosome Location	chr1:209929453-209929454
allele	G/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	TAF1	chr1:209929171-209929668	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:209929084-209933092	GM18505	blood:	n/a	n/a
3	NFIC	chr1:209929116-209929783	GM12878	blood:	n/a	n/a
4	RCOR1	chr1:209928960-209930409	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:209928692-209932543	GM12891	blood:	n/a	n/a
6	POLR2A	chr1:209929004-209931083	GM12892	blood:	n/a	n/a
7	SPI1	chr1:209929156-209929693	HL-60	blood:	n/a	chr1:209929416-209929429
8	POLR2A	chr1:209929252-209929729	GM12891	blood:	n/a	n/a
9	POLR2A	chr1:209929113-209930511	HL-60	blood:	n/a	n/a
10	PML	chr1:209929099-209930052	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:209928989-209931083	GM12892	blood:	n/a	n/a
12	TCF3	chr1:209929334-209929555	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:209929135-209930430	GM12891	blood:	n/a	n/a
14	EBF1	chr1:209929168-209930514	GM12878	blood:	n/a	chr1:209929739-209929748
15	SPI1	chr1:209929295-209929516	K562	blood:	n/a	chr1:209929416-209929429
16	POLR2A	chr1:209929144-209930769	GM12878	blood:	n/a	n/a
17	ETS1	chr1:209929217-209929657	GM12878	blood:	n/a	n/a
18	POU2F2	chr1:209929206-209929757	GM12891	blood:	n/a	n/a
19	YY1	chr1:209929205-209929763	GM12892	blood:	n/a	n/a
20	WRNIP1	chr1:209929394-209931411	GM12878	blood:	n/a	n/a
21	SPI1	chr1:209929193-209929656	GM12878	blood:	n/a	chr1:209929416-209929429
22	POLR2A	chr1:209929265-209929794	GM12878	blood:	n/a	n/a
23	BCLAF1	chr1:209929104-209929760	GM12878	blood:	n/a	n/a
24	RELA	chr1:209928787-209930749	GM19099	blood:	n/a	chr1:209928807-209928816 chr1:209928807-209928816
25	POLR2A	chr1:209929032-209933590	GM12878	blood:	n/a	n/a
26	YY1	chr1:209929346-209929668	GM12892	blood:	n/a	n/a
27	TAF1	chr1:209929290-209929625	GM12891	blood:	n/a	n/a
28	RUNX3	chr1:209928960-209930858	GM12878	blood:	n/a	chr1:209929212-209929221 chr1:209929212-209929221
29	RUNX3	chr1:209928948-209930753	GM12878	blood:	n/a	chr1:209929212-209929221 chr1:209929212-209929221
30	POLR2A	chr1:209929143-209930855	GM12892	blood:	n/a	n/a
31	POLR2A	chr1:209929173-209929820	GM12891	blood:	n/a	n/a
32	TBL1XR1	chr1:209929010-209930486	GM12878	blood:	n/a	n/a
33	TBP	chr1:209929015-209930614	GM12878	blood:	n/a	n/a
34	EBF1	chr1:209929234-209930686	GM12878	blood:	n/a	chr1:209929739-209929748
35	POLR2A	chr1:209929141-209930623	GM15510	blood:	n/a	n/a
36	SPI1	chr1:209929147-209929692	GM12891	blood:	n/a	chr1:209929416-209929429
37	CTCF	chr1:209929400-209929550	GM12868	blood:	n/a	n/a
38	POLR2A	chr1:209929232-209930682	GM12878	blood:	n/a	n/a
39	RELA	chr1:209928660-209930846	GM18951	blood:	n/a	chr1:209928807-209928816 chr1:209928807-209928816
40	PML	chr1:209929303-209929808	GM12878	blood:	n/a	n/a
41	YY1	chr1:209929299-209929675	GM12891	blood:	n/a	n/a
42	POU2F2	chr1:209929329-209929652	GM12878	blood:	n/a	n/a
43	YY1	chr1:209929277-209929662	GM12878	blood:	n/a	n/a
44	MYC	chr1:209929261-209929671	NB4	blood:	n/a	n/a
45	POLR2A	chr1:209929305-209929772	GM12878	blood:	n/a	n/a
46	SPI1	chr1:209929122-209929815	HL-60	blood:	n/a	chr1:209929416-209929429
47	BATF	chr1:209929263-209929670	GM12878	blood:	n/a	n/a
48	MAX	chr1:209929171-209930896	NB4	blood:	n/a	n/a
49	FOXM1	chr1:209929212-209929710	GM12878	blood:	n/a	n/a
50	YY1	chr1:209929199-209929755	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
TRAF3IP3	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10082248	1.00[CEU][hapmap]
rs10489343	1.00[AFR][1000 genomes]
rs10779514	1.00[AFR][1000 genomes]
rs10779515	1.00[AFR][1000 genomes]
rs10863789	1.00[AFR][1000 genomes]
rs10863790	1.00[AFR][1000 genomes]
rs1109430	1.00[AFR][1000 genomes]
rs11119345	0.85[EUR][1000 genomes]
rs11119347	1.00[AFR][1000 genomes]
rs11119348	1.00[AFR][1000 genomes]
rs11119360	1.00[AFR][1000 genomes]
rs11585733	1.00[AFR][1000 genomes]
rs11589335	1.00[AFR][1000 genomes]
rs12058100	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12062600	1.00[AFR][1000 genomes]
rs12063989	1.00[AFR][1000 genomes]
rs12064085	1.00[AFR][1000 genomes]
rs12064211	1.00[AFR][1000 genomes]
rs12064398	1.00[AFR][1000 genomes]
rs12066340	1.00[AFR][1000 genomes]
rs12069187	1.00[AFR][1000 genomes]
rs12081405	1.00[AFR][1000 genomes]
rs12405750	1.00[AFR][1000 genomes]
rs12561766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12563527	1.00[AFR][1000 genomes]
rs12566152	1.00[AFR][1000 genomes]
rs13306422	1.00[AFR][1000 genomes]
rs17015076	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17015078	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17015255	1.00[AFR][1000 genomes]
rs17015268	1.00[AFR][1000 genomes]
rs17388240	1.00[AFR][1000 genomes]
rs1856161	1.00[AFR][1000 genomes]
rs1883332	1.00[AFR][1000 genomes]
rs2038053	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2076149	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2076151	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2142860	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235370	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2235371	1.00[AFR][1000 genomes]
rs2235377	1.00[AFR][1000 genomes]
rs2236902	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2282740	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2294406	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298930	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3753517	1.00[AFR][1000 genomes]
rs41274836	1.00[AFR][1000 genomes]
rs4329516	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs4545339	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4844488	0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes]
rs4844491	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4844494	1.00[AFR][1000 genomes]
rs4844496	1.00[AFR][1000 genomes]
rs4844893	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4844894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4844908	1.00[AFR][1000 genomes]
rs56822893	0.85[EUR][1000 genomes]
rs57283682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58788672	0.83[EUR][1000 genomes]
rs6540547	1.00[CEU][hapmap]
rs6694238	1.00[CEU][hapmap]
rs7515014	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7517461	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7528642	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7532021	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs846908	1.00[CEU][hapmap]

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:47 , 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	chr1:209928600-209929600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:209928600-209932000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr1:209928600-209932200	Flanking Active TSS	GM12878-XiMat	blood
12	chr1:209928800-209930400	Flanking Active TSS	Dnd41	blood
13	chr1:209928800-209931000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr1:209928800-209932200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr1:209928800-209932400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr1:209929000-209931200	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr1:209929000-209931800	Active TSS	Duodenum Mucosa	Duodenum
18	chr1:209929000-209932000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr1:209929000-209932200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:209929000-209932200	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr1:209929000-209932400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:209929000-209932800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:209929200-209929600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:209929200-209930800	Active TSS	Primary T cells from cord blood	blood
25	chr1:209929200-209931200	Flanking Active TSS	Primary B cells from peripheral blood	blood
26	chr1:209929200-209931400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:209929200-209931400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr1:209929400-209929600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr1:209929400-209929600	Active TSS	Adipose Nuclei	Adipose
30	chr1:209929400-209929800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr1:209929400-209929800	Flanking Active TSS	Fetal Intestine Large	intestine
32	chr1:209929400-209929800	Flanking Active TSS	Fetal Intestine Small	intestine
33	chr1:209929400-209930000	Enhancers	Gastric	stomach
34	chr1:209929400-209930200	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
35	chr1:209929400-209930400	Active TSS	Thymus	Thymus
36	chr1:209929400-209930800	Active TSS	Fetal Thymus	thymus
37	chr1:209929400-209931000	Active TSS	Primary T cells fromperipheralblood	blood
38	chr1:209929400-209931000	Active TSS	Liver	Liver
39	chr1:209929400-209931000	Active TSS	Rectal Mucosa Donor 31	rectum
40	chr1:209929400-209931200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:209929400-209931200	Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr1:209929400-209931200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:209929400-209931400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
44	chr1:209929400-209931400	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr1:209929400-209931400	Active TSS	Colonic Mucosa	Colon
46	chr1:209929400-209931800	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr1:209929400-209931800	Active TSS	Rectal Smooth Muscle	rectum

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