Variant report

Variant	rs11799437
Chromosome Location	chr1:86862390-86862391
allele	A/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	CREB1	chr1:86861414-86862394	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:86861463-86862475	GM18951	blood:	n/a	n/a
3	TAF1	chr1:86861463-86862466	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:86860834-86862483	SK-N-MC	brain:	n/a	n/a
5	NFYB	chr1:86861868-86862500	Hela-S3	cervix:	n/a	chr1:86862050-86862065 chr1:86862048-86862063 chr1:86862048-86862063
6	POLR2A	chr1:86860715-86862399	PANC-1	pancreas:	n/a	n/a
7	MAX	chr1:86861434-86862398	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr1:86861546-86862412	GM12878	blood:	n/a	n/a
9	MAZ	chr1:86861362-86862825	GM12878	blood:	n/a	n/a
10	SIN3A	chr1:86861144-86862469	H1-hESC	embryonic stem cell:	n/a	chr1:86862072-86862085
11	MXI1	chr1:86860760-86863066	SK-N-SH	brain:	n/a	chr1:86861997-86862012
12	REST	chr1:86860811-86862757	H1-neurons	neurons:	n/a	chr1:86862115-86862128
13	E2F6	chr1:86861266-86862451	H1-hESC	embryonic stem cell:	n/a	chr1:86862314-86862323
14	MXI1	chr1:86861641-86862466	GM12878	blood:	n/a	chr1:86861997-86862012
15	MAX	chr1:86861537-86862450	SK-N-SH	brain:	n/a	n/a
16	CREB1	chr1:86861373-86862582	GM12878	blood:	n/a	n/a
17	SPI1	chr1:86862329-86862495	GM12878	blood:	n/a	n/a
18	IRF1	chr1:86862356-86862462	K562	blood:	n/a	n/a
19	POLR2A	chr1:86861595-86862477	PBDE	blood:	n/a	n/a
20	MAX	chr1:86861381-86862630	NB4	blood:	n/a	n/a
21	PML	chr1:86861393-86862482	GM12878	blood:	n/a	chr1:86861998-86862006
22	ELK1	chr1:86861633-86862473	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:86861004-86862445	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr1:86861316-86862497	GM18505	blood:	n/a	n/a
25	POLR2A	chr1:86861090-86862463	H1-hESC	embryonic stem cell:	n/a	n/a
26	SPI1	chr1:86862303-86862510	GM12891	blood:	n/a	n/a
27	MAX	chr1:86861926-86862401	A549	lung:	n/a	n/a
28	MAZ	chr1:86861254-86862746	IMR90	lung:	n/a	n/a
29	POLR2A	chr1:86860956-86862655	MCF10A-Er-Src	breast:	n/a	n/a
30	BRCA1	chr1:86861517-86862524	Hela-S3	cervix:	n/a	n/a
31	GTF2F1	chr1:86861007-86862423	Hela-S3	cervix:	n/a	n/a
32	ZNF143	chr1:86861652-86862635	GM12878	blood:	n/a	chr1:86862019-86862037
33	POLR2A	chr1:86860904-86862861	GM12891	blood:	n/a	n/a
34	RFX5	chr1:86860820-86862756	SK-N-SH	brain:	n/a	n/a
35	KAP1	chr1:86861619-86862416	HEK293	kidney:	n/a	chr1:86861998-86862006
36	MXI1	chr1:86861610-86862493	Hela-S3	cervix:	n/a	chr1:86861997-86862012
37	MAX	chr1:86861466-86862535	GM12878	blood:	n/a	n/a
38	BHLHE40	chr1:86861679-86862788	GM12878	blood:	n/a	n/a
39	CHD2	chr1:86861368-86862624	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:86861375-86862577	H1-neurons	neurons:	n/a	n/a
41	SPI1	chr1:86862160-86862652	HL-60	blood:	n/a	n/a
42	POLR2A	chr1:86861443-86862525	GM12878	blood:	n/a	n/a
43	MTA3	chr1:86861183-86862438	GM12878	blood:	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: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10782571	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10873771	0.90[EUR][1000 genomes]
rs10873772	0.92[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10873773	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10873774	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10873775	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10873776	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10873778	1.00[CEU][hapmap];0.80[CHD][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs10873779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1116108	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1116109	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11161803	0.92[EUR][1000 genomes]
rs11161804	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11161805	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11161806	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11161807	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11161811	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11161813	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11802019	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11810689	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12028714	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12031536	0.92[EUR][1000 genomes]
rs12033867	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12046485	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12131620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12138401	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1407719	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1407720	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1413427	0.95[CEU][hapmap]
rs1413429	0.91[CEU][hapmap]
rs16908	0.95[CEU][hapmap]
rs17372196	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1830675	0.86[EUR][1000 genomes]
rs1999600	1.00[CEU][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs2031136	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2093612	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2273941	0.95[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2273942	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2275000	0.90[EUR][1000 genomes]
rs2275001	0.91[CEU][hapmap]
rs2390057	0.82[CEU][hapmap]
rs2390096	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2390097	0.84[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2390098	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2390099	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28782251	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35173920	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3737159	0.95[CEU][hapmap]
rs3737672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3765986	0.91[CEU][hapmap]
rs3945233	0.95[CEU][hapmap]
rs4534352	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4638096	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4656026	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4656044	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4656064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656066	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58200516	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6658025	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6674140	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6679600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6703576	0.97[EUR][1000 genomes]
rs67799288	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7415758	0.95[CEU][hapmap]
rs7515651	0.92[ASW][hapmap];0.96[CEU][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7541004	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7553685	0.95[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7554545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs956499	0.95[CEU][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:123 , 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	chr1:86859800-86862400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:86859800-86862800	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr1:86860200-86862400	Active TSS	HMEC	breast
5	chr1:86860200-86862600	Active TSS	NHLF	lung
6	chr1:86860200-86862800	Active TSS	Right Atrium	heart
7	chr1:86860400-86862400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr1:86860400-86862400	Active TSS	NHDF-Ad	bronchial
9	chr1:86860400-86862600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:86860600-86862600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:86860800-86862400	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr1:86860800-86862400	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr1:86860800-86862400	Active TSS	Brain Angular Gyrus	brain
14	chr1:86860800-86862400	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr1:86860800-86862400	Active TSS	Esophagus	oesophagus
16	chr1:86860800-86862600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr1:86860800-86862600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:86860800-86862600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:86860800-86862600	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:86860800-86862600	Active TSS	Fetal Intestine Large	intestine
21	chr1:86860800-86862600	Active TSS	Fetal Kidney	kidney
22	chr1:86860800-86862800	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr1:86860800-86862800	Active TSS	HSMMtube	muscle
24	chr1:86860800-86863000	Active TSS	Colonic Mucosa	Colon
25	chr1:86861000-86862400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:86861000-86862400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:86861000-86862400	Active TSS	Thymus	Thymus
28	chr1:86861000-86862600	Active TSS	Fetal Muscle Trunk	muscle
29	chr1:86861000-86862600	Active TSS	Left Ventricle	heart
30	chr1:86861000-86862600	Active TSS	Lung	lung
31	chr1:86861000-86862600	Active TSS	Ovary	ovary
32	chr1:86861000-86862600	Active TSS	Pancreas	Pancrea
33	chr1:86861000-86862600	Active TSS	Rectal Smooth Muscle	rectum
34	chr1:86861000-86862600	Active TSS	A549	lung
35	chr1:86861000-86862800	Active TSS	Psoas Muscle	Psoas
36	chr1:86861200-86862400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:86861200-86862400	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr1:86861200-86862400	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr1:86861200-86862400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:86861200-86862400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:86861200-86862400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:86861200-86862400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:86861200-86862400	Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr1:86861200-86862400	Active TSS	Brain Cingulate Gyrus	brain
45	chr1:86861200-86862400	Active TSS	Brain Germinal Matrix	brain
46	chr1:86861200-86862400	Active TSS	Small Intestine	intestine
47	chr1:86861200-86862600	Active TSS	H1 Cell Line	embryonic stem cell
48	chr1:86861200-86862600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:86861200-86862600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:86861200-86862600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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