Variant report

Variant	rs3737671
Chromosome Location	chr1:86861843-86861844
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	CREB1	chr1:86861414-86862394	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:86861463-86862475	GM18951	blood:	n/a	n/a
3	YY1	chr1:86861588-86862010	GM12878	blood:	n/a	n/a
4	TAF1	chr1:86861463-86862466	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr1:86861800-86861950	HBMEC	blood vessel:	n/a	n/a
6	POLR2A	chr1:86861558-86862152	GM12878	blood:	n/a	n/a
7	MAX	chr1:86861650-86862345	A549	lung:	n/a	n/a
8	TCF12	chr1:86861506-86862259	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr1:86860834-86862483	SK-N-MC	brain:	n/a	n/a
10	CTCF	chr1:86861780-86861930	WERI-Rb-1	eye:	n/a	n/a
11	POLR2A	chr1:86860715-86862399	PANC-1	pancreas:	n/a	n/a
12	NFIC	chr1:86861623-86862152	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:86861136-86862293	HEK293	kidney:	n/a	n/a
14	TAF1	chr1:86861637-86862107	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr1:86861434-86862398	ECC-1	luminal epithelium:	n/a	n/a
16	YY1	chr1:86861666-86862030	A549	lung:	n/a	n/a
17	ZBTB7A	chr1:86861425-86861847	K562	blood:	n/a	chr1:86861579-86861590
18	MXI1	chr1:86861598-86862116	H1-hESC	embryonic stem cell:	n/a	chr1:86861997-86862012
19	POLR2A	chr1:86861503-86862140	GM12878	blood:	n/a	n/a
20	CTCF	chr1:86861820-86861970	SK-N-SH_RA	brain:	n/a	n/a
21	SIN3AK20	chr1:86861708-86862169	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr1:86861033-86862383	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr1:86861546-86862412	GM12878	blood:	n/a	n/a
24	EGR1	chr1:86861515-86862002	GM12878	blood:	n/a	chr1:86861568-86861581 chr1:86861582-86861592
25	CREB1	chr1:86861487-86862292	ECC-1	luminal epithelium:	n/a	n/a
26	RUNX3	chr1:86861413-86862267	GM12878	blood:	n/a	n/a
27	MAZ	chr1:86861362-86862825	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:86861579-86862200	MCF-7	breast:	n/a	n/a
29	PAX5	chr1:86861667-86862228	GM12891	blood:	n/a	n/a
30	SIN3A	chr1:86861144-86862469	H1-hESC	embryonic stem cell:	n/a	chr1:86862072-86862085
31	RFX5	chr1:86861825-86862246	GM12878	blood:	n/a	n/a
32	REST	chr1:86861360-86862117	PANC-1	pancreas:	n/a	n/a
33	SMARCC1	chr1:86861046-86862370	Hela-S3	cervix:	n/a	n/a
34	ZBTB7A	chr1:86861203-86862017	ECC-1	luminal epithelium:	n/a	chr1:86861579-86861590
35	YY1	chr1:86861548-86862197	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:86861479-86862237	GM12892	blood:	n/a	n/a
37	PAX5	chr1:86861799-86862035	GM12878	blood:	n/a	n/a
38	POLR2A	chr1:86861474-86862183	GM12878	blood:	n/a	n/a
39	EBF1	chr1:86861832-86862292	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:86861467-86862334	HL-60	blood:	n/a	n/a
41	POLR2A	chr1:86861438-86862344	Raji	blood:	n/a	n/a
42	POLR2A	chr1:86861606-86862097	U87	brain:	n/a	n/a
43	POLR2A	chr1:86861430-86862162	Gliobla	brain:	n/a	n/a
44	CTCF	chr1:86861760-86861910	AG10803	skin:	n/a	n/a
45	JUND	chr1:86861701-86861960	H1-hESC	embryonic stem cell:	n/a	n/a
46	MXI1	chr1:86860760-86863066	SK-N-SH	brain:	n/a	chr1:86861997-86862012
47	MYC	chr1:86861774-86862356	MCF10A-Er-Src	breast:	n/a	n/a
48	REST	chr1:86860811-86862757	H1-neurons	neurons:	n/a	chr1:86862115-86862128
49	POLR2A	chr1:86861462-86862161	MCF-7	breast:	n/a	n/a
50	MYC	chr1:86861782-86862316	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86821077..86823352-chr1:86861196..86863227,2	K562	blood:

Variant related genes	Relation type
ODF2L	TF binding region
ENSG00000122417	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11161808	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161833	0.84[JPT][hapmap]
rs12022446	0.83[AMR][1000 genomes]
rs12023726	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12023799	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12029568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12030666	1.00[AMR][1000 genomes]
rs12032435	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12034967	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12037028	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12037391	0.83[AMR][1000 genomes]
rs12038144	0.83[AMR][1000 genomes]
rs12038844	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12039899	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12042822	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12043873	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12044970	0.83[AMR][1000 genomes]
rs12045012	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12045465	0.83[AMR][1000 genomes]
rs12046199	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12046894	0.83[AMR][1000 genomes]
rs12047304	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12047305	0.84[ASN][1000 genomes]
rs12047913	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12048082	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12048329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12747430	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs2274999	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28688345	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28788025	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34204564	0.86[ASN][1000 genomes]
rs36096788	0.85[ASN][1000 genomes]
rs3765509	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3765984	0.85[ASN][1000 genomes]
rs3765987	0.89[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs3820038	0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3820041	0.85[ASN][1000 genomes]
rs4497186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4656103	0.85[ASN][1000 genomes]
rs55812833	0.89[ASN][1000 genomes]
rs55825812	0.89[ASN][1000 genomes]
rs55857117	0.95[ASN][1000 genomes]
rs56187142	0.89[ASN][1000 genomes]
rs57955693	0.95[ASN][1000 genomes]
rs58658794	0.95[ASN][1000 genomes]
rs59775624	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs969788	0.84[JPT][hapmap]

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	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86859600-86862800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:86859800-86862200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:86859800-86862400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:86859800-86862800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:86860200-86862400	Active TSS	HMEC	breast
6	chr1:86860200-86862600	Active TSS	NHLF	lung
7	chr1:86860200-86862800	Active TSS	Right Atrium	heart
8	chr1:86860400-86862400	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr1:86860400-86862400	Active TSS	NHDF-Ad	bronchial
10	chr1:86860400-86862600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:86860600-86862600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:86860800-86862400	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr1:86860800-86862400	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr1:86860800-86862400	Active TSS	Brain Angular Gyrus	brain
15	chr1:86860800-86862400	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr1:86860800-86862400	Active TSS	Esophagus	oesophagus
17	chr1:86860800-86862600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr1:86860800-86862600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:86860800-86862600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:86860800-86862600	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr1:86860800-86862600	Active TSS	Fetal Intestine Large	intestine
22	chr1:86860800-86862600	Active TSS	Fetal Kidney	kidney
23	chr1:86860800-86862800	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr1:86860800-86862800	Active TSS	HSMMtube	muscle
25	chr1:86860800-86863000	Active TSS	Colonic Mucosa	Colon
26	chr1:86861000-86862200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:86861000-86862200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:86861000-86862200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:86861000-86862200	Active TSS	Gastric	stomach
30	chr1:86861000-86862400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:86861000-86862400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:86861000-86862400	Active TSS	Thymus	Thymus
33	chr1:86861000-86862600	Active TSS	Fetal Muscle Trunk	muscle
34	chr1:86861000-86862600	Active TSS	Left Ventricle	heart
35	chr1:86861000-86862600	Active TSS	Lung	lung
36	chr1:86861000-86862600	Active TSS	Ovary	ovary
37	chr1:86861000-86862600	Active TSS	Pancreas	Pancrea
38	chr1:86861000-86862600	Active TSS	Rectal Smooth Muscle	rectum
39	chr1:86861000-86862600	Active TSS	A549	lung
40	chr1:86861000-86862800	Active TSS	Psoas Muscle	Psoas
41	chr1:86861200-86862200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:86861200-86862200	Active TSS	Fetal Intestine Small	intestine
43	chr1:86861200-86862200	Active TSS	Spleen	Spleen
44	chr1:86861200-86862200	Active TSS	HSMM	muscle
45	chr1:86861200-86862200	Active TSS	K562	blood
46	chr1:86861200-86862400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:86861200-86862400	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr1:86861200-86862400	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr1:86861200-86862400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:86861200-86862400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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