Variant report

Variant	rs2961684
Chromosome Location	chr5:177652086-177652087
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	chr5:177651554-177652119	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr5:177649760-177653014	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr5:177650392-177652772	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:177650707-177652879	K562	blood:	n/a	n/a
5	POLR2A	chr5:177651745-177652373	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr5:177651108-177652161	HCT-116	colon:	n/a	n/a
7	POLR2A	chr5:177647806-177652259	GM12891	blood:	n/a	n/a
8	POLR2A	chr5:177647467-177652584	HepG2	liver:	n/a	n/a
9	POLR2A	chr5:177647972-177652526	GM12878	blood:	n/a	n/a
10	POLR2A	chr5:177647479-177653078	K562	blood:	n/a	n/a
11	POLR2A	chr5:177649681-177652419	K562	blood:	n/a	n/a
12	POLR2A	chr5:177652025-177652379	HepG2	liver:	n/a	n/a
13	POLR2A	chr5:177648029-177652545	GM12878	blood:	n/a	n/a
14	POLR2A	chr5:177647699-177653070	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr5:177647352-177652340	GM12892	blood:	n/a	n/a
16	POLR2A	chr5:177651988-177652147	HepG2	liver:	n/a	n/a
17	POLR2A	chr5:177651839-177652359	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr5:177648141-177652962	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr5:177648073-177652554	HL-60	blood:	n/a	n/a
20	POLR2A	chr5:177647476-177652787	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr5:177652073-177652473	K562	blood:	n/a	n/a
22	POLR2A	chr5:177645181-177652644	A549	lung:	n/a	n/a
23	POLR2A	chr5:177647525-177652315	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
PHYKPL	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2913869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961676	0.92[YRI][hapmap]
rs2961677	0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv482872	chr5:177580298-177744381	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers 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	106 gene(s)	inside rSNPs	diseases
5	nsv1021981	chr5:177620372-177825272	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
6	nsv537967	chr5:177620372-177825272	Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
7	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177634400-177654200	Strong transcription	Fetal Stomach	stomach
2	chr5:177635800-177657000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr5:177636000-177654000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:177639400-177657600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:177640400-177655600	Weak transcription	Right Atrium	heart
6	chr5:177642600-177654200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:177643400-177656400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:177643600-177654400	Weak transcription	Aorta	Aorta
9	chr5:177643600-177655200	Weak transcription	Stomach Mucosa	stomach
10	chr5:177643800-177652200	Strong transcription	Liver	Liver
11	chr5:177643800-177653800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:177644200-177654800	Weak transcription	NHDF-Ad	bronchial
13	chr5:177645400-177654800	Strong transcription	Hela-S3	cervix
14	chr5:177645400-177656800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr5:177645400-177656800	Strong transcription	Dnd41	blood
16	chr5:177645600-177654800	Weak transcription	HSMM	muscle
17	chr5:177646000-177654400	Weak transcription	Colon Smooth Muscle	Colon
18	chr5:177646200-177654000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr5:177646200-177657000	Weak transcription	Fetal Brain Male	brain
20	chr5:177646600-177653000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:177646600-177657400	Strong transcription	Thymus	Thymus
22	chr5:177646800-177654400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:177646800-177658000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:177647400-177652400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr5:177647600-177653200	Strong transcription	A549	lung
26	chr5:177647600-177654400	Genic enhancers	Fetal Intestine Small	intestine
27	chr5:177647800-177652600	Strong transcription	Stomach Smooth Muscle	stomach
28	chr5:177647800-177653000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:177647800-177657000	Strong transcription	Brain Germinal Matrix	brain
30	chr5:177648000-177654400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:177648000-177656000	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr5:177648000-177656800	Strong transcription	Primary B cells from cord blood	blood
33	chr5:177648000-177658000	Strong transcription	Fetal Thymus	thymus
34	chr5:177648200-177653000	Strong transcription	Brain Anterior Caudate	brain
35	chr5:177648200-177654800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:177648200-177657000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:177648200-177657000	Strong transcription	NHLF	lung
38	chr5:177648200-177657400	Strong transcription	Fetal Brain Female	brain
39	chr5:177648200-177657800	Genic enhancers	Fetal Intestine Large	intestine
40	chr5:177648400-177654600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr5:177648400-177654800	Strong transcription	NHEK	skin
42	chr5:177648400-177655000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr5:177648600-177656400	Strong transcription	GM12878-XiMat	blood
44	chr5:177648600-177658000	Strong transcription	Spleen	Spleen
45	chr5:177649000-177654400	Weak transcription	Fetal Kidney	kidney
46	chr5:177649000-177655000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr5:177649000-177657400	Strong transcription	Primary T cells from cord blood	blood
48	chr5:177649200-177653200	Strong transcription	K562	blood
49	chr5:177649200-177654400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:177649400-177652200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links