Variant report

Variant	rs62391835
Chromosome Location	chr6:29717478-29717479
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:29716473-29717834	PFSK-1	brain:	n/a	n/a
2	BHLHE40	chr6:29716713-29717497	GM12878	blood:	n/a	n/a
3	SIN3A	chr6:29715713-29717573	H1-hESC	embryonic stem cell:	n/a	chr6:29717251-29717262 chr6:29717074-29717085
4	RELA	chr6:29716550-29717846	GM15510	blood:	n/a	n/a
5	POLR2A	chr6:29716547-29717491	GM18505	blood:	n/a	n/a
6	JUND	chr6:29717270-29717830	K562	blood:	n/a	chr6:29717659-29717668
7	POLR2A	chr6:29717395-29717549	HepG2	liver:	n/a	n/a
8	POLR2A	chr6:29717477-29717569	K562	blood:	n/a	n/a
9	HCFC1	chr6:29716302-29717779	K562	blood:	n/a	n/a
10	POLR2A	chr6:29716603-29717501	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:29717475-29717525	NT2-D1	testis:	n/a
2	chr6:29717475-29717525	GM06990	blood:	n/a
3	chr6:29717475-29717525	PANC-1	pancreas:	n/a
4	chr6:29717475-29717525	RPTEC	kidney:	n/a
5	chr6:29717475-29717525	K562	blood:	n/a
6	chr6:29717475-29717525	SK-N-MC	brain:	n/a
7	chr6:29717475-29717525	AG09309	skin:	n/a
8	chr6:29717475-29717525	PFSK-1	brain:	n/a
9	chr6:29717475-29717525	A549	lung:	n/a
10	chr6:29717475-29717525	HPAEpiC	pulmonary alveolar:	n/a
11	chr6:29717475-29717525	T-47D	breast:	n/a
12	chr6:29717475-29717525	NHBE	bronchial:	n/a
13	chr6:29717475-29717525	BJ	skin:	n/a
14	chr6:29717475-29717525	HMEC	breast:	n/a
15	chr6:29717475-29717525	Jurkat	blood:	n/a
16	chr6:29717475-29717525	NHDF-neo	bronchial:	n/a
17	chr6:29717475-29717525	SK-N-SH_RA	brain:	n/a
18	chr6:29717475-29717525	HNPCEpiC	eye:	n/a
19	chr6:29717475-29717525	CMK	blood:	n/a
20	chr6:29717475-29717525	AG09319	gingival:	n/a
21	chr6:29717475-29717525	HCM	heart:	n/a
22	chr6:29717475-29717525	AoSMC	blood vessel:	n/a
23	chr6:29717475-29717525	LNCaP	prostate:	n/a
24	chr6:29717475-29717525	H1-hESC	embryonic stem cell:	embryo
25	chr6:29717475-29717525	SKMC	muscle:	n/a
26	chr6:29717475-29717525	GM12878	blood:	n/a
27	chr6:29717475-29717525	HRPEpiC	eye:	n/a
28	chr6:29717475-29717525	HCT-116	colon:	n/a
29	chr6:29717475-29717525	HUVEC	blood vessel:	n/a
30	chr6:29717475-29717525	HEEpiC	esophagus:	n/a
31	chr6:29717475-29717525	HRCEpiC	kidney:	n/a
32	chr6:29717475-29717525	AG04450	lung:	fetal
33	chr6:29717475-29717525	NH-A	brain:	n/a
34	chr6:29717475-29717525	ProgFib	skin:	n/a
35	chr6:29717475-29717525	ovcar-3	ovarian:	n/a
36	chr6:29717475-29717525	SK-N-SH	brain:	n/a
37	chr6:29717475-29717525	BE2_C	brain:	n/a
38	chr6:29717475-29717525	U87	brain:	n/a
39	chr6:29717475-29717525	HepG2	liver:	n/a
40	chr6:29717475-29717525	GM19239	blood:	n/a
41	chr6:29717475-29717525	AG04449	skin:	fetal
42	chr6:29717475-29717525	HIPEpiC	eye:	n/a
43	chr6:29717475-29717525	HL-60	blood:	n/a
44	chr6:29717475-29717525	ECC-1	luminal epithelium:	n/a
45	chr6:29717475-29717525	HCF	heart:	n/a
46	chr6:29717475-29717525	SAEC	small airway:	n/a
47	chr6:29717475-29717525	Caco-2	colon:	n/a
48	chr6:29717475-29717525	GM12892	blood:	n/a
49	chr6:29717475-29717525	Hepatocyte	liver:	n/a
50	chr6:29717475-29717525	IMR90	lung:	fetal

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29716316..29718223-chr6:29719581..29721724,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000199290	TF binding region
MICE	TF binding region
HLA-F-AS1	TF binding region
ENSG00000199290	CpG island
HLA-F-AS1	CpG island
MICE	CpG island
ENSG00000272236	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs16895757	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17179010	0.84[ASN][1000 genomes]
rs17179017	0.83[ASN][1000 genomes]
rs17179038	0.83[ASN][1000 genomes]
rs17179066	0.83[ASN][1000 genomes]
rs17184661	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17185440	0.83[ASN][1000 genomes]
rs17185447	0.83[ASN][1000 genomes]
rs2394172	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs29233	1.00[AFR][1000 genomes]
rs29254	1.00[AFR][1000 genomes]
rs3888722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3906306	1.00[AFR][1000 genomes]
rs4085262	1.00[AFR][1000 genomes]
rs4085264	1.00[AFR][1000 genomes]
rs4143366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55661776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55672647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55693745	1.00[AFR][1000 genomes]
rs55729140	0.83[ASN][1000 genomes]
rs55791644	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55792521	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55884048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55933609	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55970611	0.83[ASN][1000 genomes]
rs56044823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56101454	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56104249	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56128518	0.84[ASN][1000 genomes]
rs56155978	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56172386	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56236016	0.84[ASN][1000 genomes]
rs56269224	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56287651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56290866	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56324548	0.83[ASN][1000 genomes]
rs56353080	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56392172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58075773	0.83[ASN][1000 genomes]
rs61609080	0.83[ASN][1000 genomes]
rs62391766	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62391767	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62391768	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62391770	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62391785	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62391786	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62391801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62391819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62391821	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62391822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62391833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62391842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62391843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62391844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62391850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62391851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62391962	0.84[ASN][1000 genomes]
rs62391963	0.84[ASN][1000 genomes]
rs62391965	0.82[ASN][1000 genomes]
rs62392946	1.00[AFR][1000 genomes]
rs62392949	1.00[AFR][1000 genomes]
rs62392950	1.00[AFR][1000 genomes]
rs62392953	1.00[AFR][1000 genomes]
rs62392954	1.00[AFR][1000 genomes]
rs62392955	1.00[AFR][1000 genomes]
rs62392956	1.00[AFR][1000 genomes]
rs62392957	1.00[AFR][1000 genomes]
rs62392958	1.00[AFR][1000 genomes]
rs62394668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62394669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62394670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62394676	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62394678	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62394681	0.84[ASN][1000 genomes]
rs62394682	0.83[ASN][1000 genomes]
rs67382831	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71550159	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv883532	chr6:29703262-29814963	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv883534	chr6:29708222-29724310	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	esv3441842	chr6:29715749-29942950	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29715400-29717600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr6:29715400-29717800	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr6:29715600-29718000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:29715800-29717600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:29715800-29717600	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr6:29715800-29717600	Bivalent/Poised TSS	Fetal Lung	lung
7	chr6:29716000-29717600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:29716000-29717600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
9	chr6:29716000-29717600	Active TSS	Primary T cells from cord blood	blood
10	chr6:29716000-29717800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:29716200-29717600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:29716200-29717600	Active TSS	Hela-S3	cervix
13	chr6:29716400-29717600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:29716400-29717800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:29716800-29717600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr6:29716800-29717600	Active TSS	Colonic Mucosa	Colon
17	chr6:29716800-29717800	Enhancers	Placenta Amnion	Placenta Amnion
18	chr6:29717000-29717600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
19	chr6:29717000-29717600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:29717000-29717600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:29717000-29717600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:29717000-29717600	Flanking Bivalent TSS/Enh	HepG2	liver
23	chr6:29717000-29717600	Flanking Active TSS	HMEC	breast
24	chr6:29717000-29717800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:29717000-29717800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr6:29717000-29718000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:29717000-29720000	Enhancers	Spleen	Spleen
28	chr6:29717200-29717600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
29	chr6:29717200-29717600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:29717200-29717600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
31	chr6:29717200-29717600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:29717200-29717600	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr6:29717200-29717600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
34	chr6:29717200-29717600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
35	chr6:29717200-29717600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr6:29717200-29717600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:29717200-29717600	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr6:29717200-29717600	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr6:29717200-29717600	Flanking Active TSS	Brain Hippocampus Middle	brain
40	chr6:29717200-29717600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr6:29717200-29717600	Flanking Active TSS	Brain Substantia Nigra	brain
42	chr6:29717200-29717600	Flanking Active TSS	Colon Smooth Muscle	Colon
43	chr6:29717200-29717600	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr6:29717200-29717600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr6:29717200-29717600	Bivalent Enhancer	Fetal Stomach	stomach
46	chr6:29717200-29717600	Enhancers	Gastric	stomach
47	chr6:29717200-29717600	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr6:29717200-29717600	Flanking Active TSS	Right Atrium	heart
49	chr6:29717200-29717600	Flanking Active TSS	Right Ventricle	heart
50	chr6:29717200-29717600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links