Variant report

Variant	rs6657364
Chromosome Location	chr1:179868470-179868471
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	STAT3	chr1:179868332-179868615	MCF10A-Er-Src	breast:	n/a	n/a
2	CEBPB	chr1:179868231-179868499	K562	blood:	n/a	chr1:179868359-179868370
3	CEBPB	chr1:179868269-179868519	HepG2	liver:	n/a	chr1:179868359-179868370

No.	Distal block	Cell Line	Cell type
1	chr1:179851104..179853394-chr1:179865735..179868796,3	K562	blood:
2	chr1:179849456..179851628-chr1:179866576..179869234,2	MCF-7	breast:
3	chr1:179845449..179848601-chr1:179867688..179872232,4	K562	blood:
4	chr1:179866999..179869091-chr1:180123672..180125577,2	MCF-7	breast:

Variant related genes	Relation type
TOR1AIP1	TF binding region
RN7SL230P	TF binding region
ENSG00000116260	Chromatin interaction
ENSG00000169905	Chromatin interaction
ENSG00000272906	Chromatin interaction
ENSG00000143337	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10913901	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913906	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1148815	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs11546310	0.94[ASN][1000 genomes]
rs12062383	0.84[GIH][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs1281378	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs1281432	0.81[TSI][hapmap]
rs1300068	0.84[GIH][hapmap]
rs17279483	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17279594	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2007148	0.81[TSI][hapmap]
rs2249346	0.81[TSI][hapmap]
rs2318388	0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3737813	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3753398	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4310406	0.83[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4651052	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs522534	0.80[EUR][1000 genomes]
rs547776	0.81[EUR][1000 genomes]
rs55706288	0.94[ASN][1000 genomes]
rs58392320	0.92[ASN][1000 genomes]
rs599185	0.81[EUR][1000 genomes]
rs605807	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs609521	0.81[EUR][1000 genomes]
rs61184002	0.92[ASN][1000 genomes]
rs612215	0.80[EUR][1000 genomes]
rs644412	0.84[GIH][hapmap]
rs6666510	0.94[ASN][1000 genomes]
rs6680290	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7411457	0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7530362	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 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	chr1:179852800-179871200	Weak transcription	Spleen	Spleen
2	chr1:179853000-179884800	Weak transcription	Esophagus	oesophagus
3	chr1:179853000-179890400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:179853200-179886600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:179853200-179890800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:179853400-179872600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:179853400-179877000	Weak transcription	Right Ventricle	heart
8	chr1:179853400-179878200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:179853400-179882800	Weak transcription	Fetal Brain Male	brain
10	chr1:179854000-179886800	Weak transcription	Fetal Heart	heart
11	chr1:179854200-179871800	Weak transcription	Brain Germinal Matrix	brain
12	chr1:179855600-179871600	Weak transcription	A549	lung
13	chr1:179856200-179876800	Weak transcription	NHLF	lung
14	chr1:179857600-179870000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:179857600-179871600	Weak transcription	HSMM	muscle
16	chr1:179857600-179886800	Weak transcription	Psoas Muscle	Psoas
17	chr1:179860000-179869800	Weak transcription	Hela-S3	cervix
18	chr1:179860000-179873800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:179860200-179890200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:179860400-179871600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:179860400-179873000	Weak transcription	HUVEC	blood vessel
22	chr1:179860400-179873200	Weak transcription	K562	blood
23	chr1:179860400-179878800	Weak transcription	Colonic Mucosa	Colon
24	chr1:179860600-179869400	Weak transcription	HMEC	breast
25	chr1:179860600-179871600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:179861000-179871400	Weak transcription	NHEK	skin
27	chr1:179861000-179871600	Weak transcription	Brain Substantia Nigra	brain
28	chr1:179861200-179869600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:179861200-179870000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:179861200-179870800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:179861200-179871400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:179861200-179878000	Weak transcription	Gastric	stomach
33	chr1:179861200-179886600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr1:179861400-179869400	Weak transcription	GM12878-XiMat	blood
35	chr1:179861400-179870400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:179861400-179871000	Weak transcription	Brain Hippocampus Middle	brain
37	chr1:179861400-179871600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:179861400-179871600	Weak transcription	Aorta	Aorta
39	chr1:179861400-179871600	Weak transcription	HSMMtube	muscle
40	chr1:179861400-179882200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:179861600-179869000	Weak transcription	Primary T cells from cord blood	blood
42	chr1:179861600-179869200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:179861600-179871400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:179861600-179871600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:179861600-179871600	Weak transcription	Thymus	Thymus
46	chr1:179861600-179871600	Weak transcription	HepG2	liver
47	chr1:179861600-179872600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:179861600-179872600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:179861600-179886600	Weak transcription	Pancreas	Pancrea
50	chr1:179862000-179870000	Weak transcription	NH-A	brain

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