Variant report

Variant	rs7646935
Chromosome Location	chr3:119042768-119042769
allele	C/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	RELA	chr3:119041704-119042771	GM19099	blood:	n/a	chr3:119042019-119042028 chr3:119042019-119042028
2	RELA	chr3:119041715-119042803	GM10847	blood:	n/a	chr3:119042019-119042028 chr3:119042019-119042028
3	POLR2A	chr3:119041124-119042804	GM12891	blood:	n/a	n/a
4	RFX5	chr3:119042372-119044133	IMR90	lung:	n/a	chr3:119043880-119043889
5	MTA3	chr3:119040824-119043149	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:119042644-119042820	H1-hESC	embryonic stem cell:	n/a	n/a
7	RUNX3	chr3:119041630-119042951	GM12878	blood:	n/a	n/a
8	TAF1	chr3:119041076-119042802	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:119040966-119042913	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr3:119040962-119042871	GM12891	blood:	n/a	n/a
11	PML	chr3:119040990-119043120	GM12878	blood:	n/a	n/a
12	CEBPB	chr3:119041662-119043052	GM12878	blood:	n/a	n/a
13	HA-E2F1	chr3:119041525-119042791	MCF-7	breast:	n/a	chr3:119041792-119041802 chr3:119042026-119042035 chr3:119042234-119042243
14	POLR2A	chr3:119040475-119042774	GM12892	blood:	n/a	n/a
15	YY1	chr3:119042223-119042769	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr3:119040990-119043033	H1-hESC	embryonic stem cell:	n/a	n/a
17	CHD1	chr3:119042269-119042831	H1-hESC	embryonic stem cell:	n/a	n/a
18	RELA	chr3:119041138-119042873	GM12891	blood:	n/a	chr3:119042019-119042028 chr3:119042019-119042028
19	RUNX3	chr3:119041127-119042892	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:119041156-119042771	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:119040381..119043387-chr3:119393976..119396207,3	K562	blood:
2	chr3:119016211..119028042-chr3:119037960..119043695,12	MCF-7	breast:
3	chr3:119041713..119043287-chr3:119530571..119533210,2	MCF-7	breast:
4	chr3:119012312..119014941-chr3:119040203..119043471,4	MCF-7	breast:
5	chr3:119011662..119015799-chr3:119040784..119043293,4	MCF-7	breast:
6	chr3:119041710..119043371-chr3:119051543..119054199,2	K562	blood:
7	chr3:119040625..119043456-chr3:119181021..119182647,3	MCF-7	breast:
8	chr3:119040520..119043561-chr3:119060040..119062334,3	MCF-7	breast:

Variant related genes	Relation type
ARHGAP31	TF binding region
ARHGAP31-AS1	TF binding region
ENSG00000207310	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000242829	Chromatin interaction
ENSG00000031081	Chromatin interaction
ENSG00000138495	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs4687849	1.00[EUR][1000 genomes]
rs4687850	1.00[EUR][1000 genomes]
rs4687999	1.00[EUR][1000 genomes]
rs6803331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72491139	1.00[AMR][1000 genomes]
rs72960637	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72960640	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72960642	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73854487	1.00[EUR][1000 genomes]
rs73854488	1.00[EUR][1000 genomes]
rs9830421	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119040600-119043000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:119040600-119043000	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr3:119040800-119042800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr3:119041000-119042800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:119041000-119042800	Active TSS	K562	blood
6	chr3:119041200-119042800	Active TSS	Fetal Kidney	kidney
7	chr3:119041200-119042800	Flanking Active TSS	HMEC	breast
8	chr3:119041600-119042800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:119041600-119042800	Active TSS	Colonic Mucosa	Colon
10	chr3:119041600-119042800	Active TSS	Stomach Smooth Muscle	stomach
11	chr3:119041600-119043000	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr3:119042000-119043200	Enhancers	Fetal Heart	heart
13	chr3:119042200-119042800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr3:119042200-119042800	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr3:119042200-119042800	Flanking Active TSS	Primary B cells from peripheral blood	blood
16	chr3:119042200-119042800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr3:119042200-119042800	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr3:119042200-119042800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:119042200-119042800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:119042200-119042800	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr3:119042200-119042800	Flanking Active TSS	Fetal Muscle Leg	muscle
22	chr3:119042200-119043000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr3:119042200-119043000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr3:119042200-119043000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:119042200-119043000	Flanking Active TSS	GM12878-XiMat	blood
26	chr3:119042400-119042800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
27	chr3:119042400-119042800	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:119042400-119042800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:119042400-119042800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr3:119042400-119042800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
31	chr3:119042400-119042800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr3:119042400-119042800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:119042400-119042800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr3:119042400-119042800	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr3:119042400-119042800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr3:119042400-119042800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr3:119042400-119042800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:119042400-119042800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr3:119042400-119042800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:119042400-119042800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:119042400-119042800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:119042400-119042800	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr3:119042400-119042800	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr3:119042400-119042800	Flanking Active TSS	Brain Germinal Matrix	brain
45	chr3:119042400-119042800	Flanking Active TSS	Colon Smooth Muscle	Colon
46	chr3:119042400-119042800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr3:119042400-119042800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr3:119042400-119042800	Flanking Active TSS	Fetal Intestine Large	intestine
49	chr3:119042400-119042800	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr3:119042400-119042800	Flanking Active TSS	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links