Variant report

Variant	rs6723188
Chromosome Location	chr2:97208158-97208159
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	POLR2A	chr2:97207729-97208318	GM12891	blood:	n/a	n/a
2	POLR2A	chr2:97207347-97208644	GM18505	blood:	n/a	n/a
3	POLR2A	chr2:97207039-97211534	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:97207187-97209166	GM12891	blood:	n/a	n/a
5	POLR2A	chr2:97207062-97210857	GM12892	blood:	n/a	n/a
6	POLR2A	chr2:97207223-97210287	GM12891	blood:	n/a	n/a
7	POLR2A	chr2:97207258-97209111	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:97207194-97211500	GM12892	blood:	n/a	n/a
9	POLR2A	chr2:97207978-97208315	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:97208092-97208308	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:97207908-97209131	GM12892	blood:	n/a	n/a
12	POLR2A	chr2:97207061-97211469	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:97207126-97210121	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:97207088-97210950	GM12892	blood:	n/a	n/a
15	WRNIP1	chr2:97208019-97208188	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:97207109-97210906	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:97207326..97209609-chr2:97211124..97214729,3	MCF-7	breast:
2	chr2:97201915..97203770-chr2:97207532..97209161,2	MCF-7	breast:
3	chr2:97201312..97206028-chr2:97206579..97208935,6	MCF-7	breast:

Variant related genes	Relation type
ARID5A	TF binding region
ENSG00000196843	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10427212	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119523	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292939	1.00[CEU][hapmap]
rs59021132	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59118112	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60378028	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60501446	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576973	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[EUR][1000 genomes]
rs6576975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715933	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719267	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs72939377	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608325	1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9752465	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3460902	chr2:97138421-97459342	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	esv3460903	chr2:97138421-97459342	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv999871	chr2:97157196-97407711	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv535829	chr2:97157196-97407711	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97203800-97220000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr2:97204200-97213200	Weak transcription	HSMMtube	muscle
3	chr2:97204400-97208200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:97204400-97213000	Weak transcription	Ovary	ovary
5	chr2:97204400-97220000	Weak transcription	HSMM	muscle
6	chr2:97204600-97215200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:97204800-97215200	Weak transcription	Liver	Liver
8	chr2:97205200-97208200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:97205200-97208400	Weak transcription	Colonic Mucosa	Colon
10	chr2:97205200-97210200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
11	chr2:97205200-97213000	Weak transcription	Gastric	stomach
12	chr2:97205200-97213200	Weak transcription	Brain Angular Gyrus	brain
13	chr2:97205200-97213200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:97205200-97214200	Weak transcription	Pancreas	Pancrea
15	chr2:97205400-97213200	Weak transcription	Fetal Lung	lung
16	chr2:97205400-97215400	Weak transcription	HepG2	liver
17	chr2:97205600-97211800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:97205600-97212200	Weak transcription	Small Intestine	intestine
19	chr2:97205600-97213000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr2:97205600-97213600	Genic enhancers	Primary T cells fromperipheralblood	blood
21	chr2:97205800-97213000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:97205800-97213200	Weak transcription	Fetal Intestine Small	intestine
23	chr2:97205800-97213400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr2:97205800-97215000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:97205800-97220000	Weak transcription	Primary B cells from cord blood	blood
26	chr2:97206000-97208200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:97206000-97211800	Weak transcription	HUVEC	blood vessel
28	chr2:97206000-97212600	Weak transcription	Right Atrium	heart
29	chr2:97206000-97213000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:97206000-97213200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:97206000-97218800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr2:97206000-97220000	Weak transcription	Fetal Heart	heart
33	chr2:97206200-97211000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:97206200-97211800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:97206200-97212000	Weak transcription	Esophagus	oesophagus
36	chr2:97206200-97212000	Strong transcription	Fetal Thymus	thymus
37	chr2:97206200-97212400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:97206200-97213000	Weak transcription	Brain Substantia Nigra	brain
39	chr2:97206200-97213200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr2:97206200-97214400	Weak transcription	Brain Anterior Caudate	brain
41	chr2:97206200-97214600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr2:97206200-97215600	Weak transcription	A549	lung
43	chr2:97206400-97208400	Weak transcription	NH-A	brain
44	chr2:97206400-97209400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr2:97206400-97211000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:97206400-97211600	Weak transcription	HMEC	breast
47	chr2:97206400-97212200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr2:97206400-97214400	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:97206600-97220000	Weak transcription	NHEK	skin
50	chr2:97206600-97222200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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