Variant report

Variant	rs71639062
Chromosome Location	chr1:161352403-161352404
allele	A/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	chr1:161352278-161352609	U87	brain:	n/a	n/a
2	CTCF	chr1:161352372-161352480	GM12878	blood:	n/a	n/a
3	CTCF	chr1:161352401-161352422	GM10248	blood:	n/a	n/a
4	FOS	chr1:161352077-161352845	MCF10A-Er-Src	breast:	n/a	chr1:161352538-161352547
5	STAT3	chr1:161351887-161353993	MCF10A-Er-Src	breast:	n/a	chr1:161352689-161352701
6	CTCF	chr1:161352365-161352482	Gliobla	brain:	n/a	n/a
7	POLR2A	chr1:161352106-161352637	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr1:161351699-161352736	A549	lung:	n/a	chr1:161352098-161352116 chr1:161352103-161352111 chr1:161352093-161352114
9	MYC	chr1:161351960-161352823	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr1:161351992-161353210	IMR90	lung:	n/a	n/a
11	STAT3	chr1:161351973-161352760	MCF10A-Er-Src	breast:	n/a	chr1:161352689-161352701
12	NR3C1	chr1:161352316-161352795	A549	lung:	n/a	chr1:161352561-161352575 chr1:161352741-161352759
13	FOS	chr1:161351993-161352645	MCF10A-Er-Src	breast:	n/a	chr1:161352538-161352547
14	POLR2A	chr1:161352271-161352614	Hela-S3	cervix:	n/a	n/a
15	FOXA2	chr1:161352259-161352709	A549	lung:	n/a	n/a
16	STAT3	chr1:161351940-161353938	MCF10A-Er-Src	breast:	n/a	chr1:161352689-161352701
17	FOS	chr1:161352000-161352875	MCF10A-Er-Src	breast:	n/a	chr1:161352538-161352547
18	CTCF	chr1:161352340-161352490	SAEC	small airway:	n/a	n/a
19	CTCF	chr1:161352394-161352454	K562	blood:	n/a	n/a
20	RAD21	chr1:161351604-161352588	SK-N-SH	brain:	n/a	chr1:161352104-161352116 chr1:161352106-161352113
21	FOS	chr1:161352030-161352915	MCF10A-Er-Src	breast:	n/a	chr1:161352538-161352547
22	STAT3	chr1:161351937-161353985	MCF10A-Er-Src	breast:	n/a	chr1:161352689-161352701
23	POLR2A	chr1:161352170-161352845	U87	brain:	n/a	n/a
24	POLR2A	chr1:161352227-161352493	HUVEC	blood vessel:	n/a	n/a
25	TAF1	chr1:161352328-161352630	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr1:161352007-161352505	SK-N-SH	brain:	n/a	n/a
27	CTCF	chr1:161351597-161352463	SK-N-SH	brain:	n/a	chr1:161352098-161352116 chr1:161352103-161352111 chr1:161352093-161352114
28	CTCF	chr1:161352380-161352510	GM20000	blood:	n/a	n/a
29	CTCF	chr1:161352349-161352503	GM13977	blood:	n/a	n/a
30	POLR2A	chr1:161352136-161352735	MCF10A-Er-Src	breast:	n/a	n/a
31	CTCF	chr1:161352388-161352475	GM19239	blood:	n/a	n/a
32	FOSL2	chr1:161351952-161352590	A549	lung:	n/a	chr1:161352538-161352547
33	POLR2A	chr1:161351637-161353936	MCF10A-Er-Src	breast:	n/a	n/a
34	MYC	chr1:161352003-161352575	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr1:161352228-161352714	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr1:161352382-161352489	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr1:161352361-161352477	GM10266	blood:	n/a	n/a
38	CTCF	chr1:161352392-161352483	Lung_OC	lung:	n/a	n/a
39	SMC3	chr1:161351945-161352441	SK-N-SH	brain:	n/a	n/a
40	CTCF	chr1:161352326-161352477	Spleen_OC	spleen:	n/a	n/a
41	FOS	chr1:161352064-161352659	HUVEC	blood vessel:	n/a	chr1:161352538-161352547

No.	Distal block	Cell Line	Cell type
1	chr1:161162025..161162580-chr1:161351852..161352505,3	K562	blood:
2	chr1:161178544..161181092-chr1:161350724..161353632,2	K562	blood:
3	chr1:161350737..161353206-chr1:161398180..161400090,2	K562	blood:
4	chr1:161352053..161353728-chr1:161407304..161409972,2	K562	blood:
5	chr1:161176175..161178205-chr1:161352097..161354818,2	K562	blood:
6	chr1:161163396..161164093-chr1:161352009..161352586,2	MCF-7	breast:
7	chr1:161352351..161353889-chr1:161357859..161359793,2	K562	blood:
8	chr1:161352260..161354753-chr1:161367912..161370247,2	K562	blood:
9	chr1:161345136..161348126-chr1:161349827..161352612,2	K562	blood:
10	chr1:161162284..161164231-chr1:161350285..161353157,2	MCF-7	breast:
11	chr1:161179255..161180597-chr1:161351619..161352560,5	K562	blood:
12	chr1:161351090..161356215-chr1:161358922..161361757,5	MCF-7	breast:
13	chr1:161281992..161284630-chr1:161351786..161353873,2	K562	blood:
14	chr1:161350529..161353664-chr1:161354181..161356756,3	K562	blood:

Variant related genes	Relation type
RRM2P2	TF binding region
ENSG00000143252	Chromatin interaction
ENSG00000158864	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10494359	1.00[ASN][1000 genomes]
rs10494360	1.00[ASN][1000 genomes]
rs11801022	1.00[ASN][1000 genomes]
rs11810143	1.00[ASN][1000 genomes]
rs12722986	1.00[ASN][1000 genomes]
rs12741391	1.00[ASN][1000 genomes]
rs12744234	1.00[ASN][1000 genomes]
rs12746613	1.00[ASN][1000 genomes]
rs12748656	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749237	1.00[ASN][1000 genomes]
rs12758795	1.00[ASN][1000 genomes]
rs17394957	1.00[ASN][1000 genomes]
rs17395595	1.00[ASN][1000 genomes]
rs17398689	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17399583	1.00[ASN][1000 genomes]
rs17400053	1.00[ASN][1000 genomes]
rs17400517	1.00[ASN][1000 genomes]
rs34006306	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34370781	1.00[ASN][1000 genomes]
rs34550741	1.00[ASN][1000 genomes]
rs35046931	1.00[ASN][1000 genomes]
rs35200803	1.00[ASN][1000 genomes]
rs35620439	1.00[ASN][1000 genomes]
rs35825219	1.00[ASN][1000 genomes]
rs35949692	1.00[ASN][1000 genomes]
rs36059328	1.00[ASN][1000 genomes]
rs3845548	1.00[ASN][1000 genomes]
rs4082014	1.00[ASN][1000 genomes]
rs55864322	1.00[ASN][1000 genomes]
rs55971447	1.00[ASN][1000 genomes]
rs56157533	1.00[ASN][1000 genomes]
rs56199187	1.00[ASN][1000 genomes]
rs61686728	1.00[ASN][1000 genomes]
rs61802846	1.00[ASN][1000 genomes]
rs66579967	1.00[ASN][1000 genomes]
rs6666989	1.00[ASN][1000 genomes]
rs6671753	1.00[ASN][1000 genomes]
rs6679543	1.00[ASN][1000 genomes]
rs66888136	1.00[ASN][1000 genomes]
rs67307769	1.00[ASN][1000 genomes]
rs67418890	1.00[ASN][1000 genomes]
rs71632979	1.00[ASN][1000 genomes]
rs71632995	1.00[ASN][1000 genomes]
rs71639056	1.00[ASN][1000 genomes]
rs72714962	1.00[ASN][1000 genomes]
rs72717013	1.00[ASN][1000 genomes]
rs72717016	1.00[ASN][1000 genomes]
rs72717018	1.00[ASN][1000 genomes]
rs72717040	1.00[ASN][1000 genomes]
rs72717048	1.00[ASN][1000 genomes]
rs7515174	1.00[ASN][1000 genomes]
rs7518087	1.00[ASN][1000 genomes]
rs7529225	1.00[ASN][1000 genomes]
rs7529425	1.00[ASN][1000 genomes]
rs7532275	1.00[ASN][1000 genomes]
rs7539468	1.00[ASN][1000 genomes]
rs7552317	1.00[ASN][1000 genomes]
rs867624	1.00[ASN][1000 genomes]
rs9427039	1.00[ASN][1000 genomes]
rs9427059	1.00[ASN][1000 genomes]
rs9427065	1.00[ASN][1000 genomes]
rs9427372	1.00[ASN][1000 genomes]
rs9427387	1.00[ASN][1000 genomes]
rs9427392	1.00[ASN][1000 genomes]
rs9427394	1.00[ASN][1000 genomes]
rs9427398	1.00[ASN][1000 genomes]
rs9427399	1.00[ASN][1000 genomes]
rs9427400	1.00[ASN][1000 genomes]
rs9427401	1.00[ASN][1000 genomes]
rs9427402	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432986	chr1:161221133-161673682	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1010776	chr1:161282384-161409218	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv432998	chr1:161335902-161673682	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv872493	chr1:161339060-161413794	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv433009	chr1:161343927-161639328	Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
6	nsv1005812	chr1:161343951-161548101	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv535182	chr1:161343951-161548101	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
8	esv2756866	chr1:161344255-161681552	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
9	esv2758972	chr1:161344255-161681552	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161327400-161352600	Weak transcription	Lung	lung
2	chr1:161328400-161359000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:161328600-161359000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:161335000-161356000	Weak transcription	K562	blood
5	chr1:161337800-161356200	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:161338000-161356000	Weak transcription	GM12878-XiMat	blood
7	chr1:161349200-161358600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:161351600-161352600	Enhancers	Primary hematopoietic stem cells	blood
9	chr1:161351600-161352600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:161351600-161352600	Enhancers	Fetal Stomach	stomach
11	chr1:161351600-161352800	Enhancers	Colon Smooth Muscle	Colon
12	chr1:161351600-161352800	Enhancers	Left Ventricle	heart
13	chr1:161351600-161352800	Enhancers	HepG2	liver
14	chr1:161351600-161353600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:161351600-161353800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:161351800-161353000	Enhancers	NHLF	lung
17	chr1:161351800-161358800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:161352000-161353400	Enhancers	Adipose Nuclei	Adipose
19	chr1:161352200-161352600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr1:161352200-161352600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:161352200-161352800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:161352200-161352800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:161352200-161352800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr1:161352200-161352800	Enhancers	Brain Cingulate Gyrus	brain
25	chr1:161352200-161352800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr1:161352200-161352800	Flanking Active TSS	A549	lung
27	chr1:161352200-161352800	Flanking Active TSS	Hela-S3	cervix
28	chr1:161352200-161352800	Flanking Active TSS	HMEC	breast
29	chr1:161352200-161352800	Enhancers	HSMM	muscle
30	chr1:161352200-161352800	Flanking Active TSS	HUVEC	blood vessel
31	chr1:161352200-161352800	Flanking Active TSS	NH-A	brain
32	chr1:161352200-161352800	Enhancers	NHDF-Ad	bronchial
33	chr1:161352200-161352800	Flanking Active TSS	Osteobl	bone
34	chr1:161352200-161353000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:161352200-161353000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:161352200-161353000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr1:161352200-161353200	Flanking Active TSS	NHEK	skin
38	chr1:161352200-161353400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:161352400-161352600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:161352400-161352600	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr1:161352400-161352800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:161352400-161355600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:161352400-161358600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:161352400-161358800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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