Variant report

Variant	rs7895468
Chromosome Location	chr10:38264700-38264701
allele	C/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	TBP	chr10:38264337-38265911	K562	blood:	n/a	n/a
2	POLR2A	chr10:38264498-38265943	Hela-S3	cervix:	n/a	n/a
3	MYC	chr10:38264645-38265858	K562	blood:	n/a	n/a
4	POLR2A	chr10:38264492-38266105	PBDE	blood:	n/a	n/a
5	NRF1	chr10:38264651-38266126	SK-N-SH	brain:	n/a	chr10:38265577-38265588 chr10:38265578-38265589 chr10:38265403-38265412 chr10:38265580-38265589 chr10:38265578-38265592 chr10:38265289-38265303
6	POLR2A	chr10:38264520-38265988	GM18505	blood:	n/a	n/a
7	SMC3	chr10:38264458-38266146	SK-N-SH	brain:	n/a	chr10:38265363-38265373
8	CHD1	chr10:38264622-38265928	GM12878	blood:	n/a	n/a
9	POLR2A	chr10:38264640-38265979	GM12878	blood:	n/a	n/a
10	MYC	chr10:38264642-38265897	MCF10A-Er-Src	breast:	n/a	n/a
11	CTCF	chr10:38264600-38264750	AG10803	skin:	n/a	n/a
12	MYC	chr10:38264220-38266048	NB4	blood:	n/a	n/a
13	CTCF	chr10:38264660-38264810	GM12871	blood:	n/a	n/a
14	MTA3	chr10:38264161-38266087	GM12878	blood:	n/a	n/a
15	POLR2A	chr10:38264006-38265982	NB4	blood:	n/a	n/a
16	MAX	chr10:38264628-38265934	A549	lung:	n/a	n/a
17	POLR2A	chr10:38264655-38264809	GM12878	blood:	n/a	n/a
18	POLR2A	chr10:38264390-38264966	GM12878	blood:	n/a	n/a
19	MAX	chr10:38264191-38266090	NB4	blood:	n/a	n/a
20	POLR2A	chr10:38264633-38266033	GM12878	blood:	n/a	n/a
21	PML	chr10:38264280-38266101	GM12878	blood:	n/a	n/a
22	POLR2A	chr10:38264352-38266040	GM12878	blood:	n/a	n/a
23	RUNX3	chr10:38264329-38264733	GM12878	blood:	n/a	chr10:38264562-38264571 chr10:38264562-38264571
24	POLR2A	chr10:38264530-38264807	GM12892	blood:	n/a	n/a
25	RCOR1	chr10:38264276-38265918	K562	blood:	n/a	n/a
26	POLR2A	chr10:38264359-38265938	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr10:38264335-38265920	HepG2	liver:	n/a	n/a
28	HCFC1	chr10:38264273-38266099	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr10:38264287-38266016	GM12891	blood:	n/a	n/a
30	POLR2A	chr10:38264332-38265997	GM12878	blood:	n/a	n/a
31	ZNF263	chr10:38264544-38266240	HEK293-T-REx	kidney:	n/a	n/a
32	POLR2A	chr10:38264579-38264820	GM12878	blood:	n/a	n/a
33	POLR2A	chr10:38264617-38265999	GM19099	blood:	n/a	n/a
34	POLR2A	chr10:38264525-38266009	GM18951	blood:	n/a	n/a
35	POLR2A	chr10:38264571-38265964	GM18526	blood:	n/a	n/a
36	POLR2A	chr10:38264659-38266003	GM12892	blood:	n/a	n/a
37	POLR2A	chr10:38264442-38266105	GM12892	blood:	n/a	n/a
38	POLR2A	chr10:38264613-38265878	HepG2	liver:	n/a	n/a
39	RUNX3	chr10:38264274-38266012	GM12878	blood:	n/a	chr10:38264562-38264571 chr10:38264562-38264571
40	TCF12	chr10:38264673-38266040	A549	lung:	n/a	n/a
41	MXI1	chr10:38264574-38265998	GM12878	blood:	n/a	n/a
42	RAD21	chr10:38264102-38266099	SK-N-SH	brain:	n/a	chr10:38265229-38265242 chr10:38265151-38265164 chr10:38265709-38265728
43	POLR2A	chr10:38264262-38266012	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr10:38264382-38265953	Raji	blood:	n/a	n/a
45	MXI1	chr10:38264451-38266051	IMR90	lung:	n/a	n/a
46	CTCF	chr10:38264377-38266234	A549	lung:	n/a	chr10:38265315-38265328 chr10:38265708-38265726 chr10:38265315-38265324 chr10:38265709-38265725 chr10:38265711-38265724
47	REST	chr10:38264202-38266267	H1-neurons	neurons:	n/a	chr10:38265720-38265729 chr10:38265354-38265367
48	YY1	chr10:38264316-38264760	SK-N-SH	brain:	n/a	chr10:38264427-38264437
49	POLR2A	chr10:38264599-38265920	K562	blood:	n/a	n/a
50	MAX	chr10:38264538-38266109	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:38242058..38244138-chr10:38263364..38265414,2	K562	blood:
2	chr10:38262821..38267029-chr10:38297888..38300843,9	MCF-7	breast:
3	chr10:38260688..38263129-chr10:38263289..38264919,2	MCF-7	breast:
4	chr10:38259521..38261309-chr10:38263503..38265407,2	MCF-7	breast:
5	chr10:38144757..38148220-chr10:38264242..38266228,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226447	TF binding region
ENSG00000189180	Chromatin interaction
ENSG00000236514	Chromatin interaction
ENSG00000266684	Chromatin interaction
ENSG00000198105	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1208578	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1208619	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1208621	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12243792	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs12265979	0.95[CEU][hapmap]
rs12413083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[ASN][1000 genomes]
rs12414618	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1735625	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17608725	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs176831	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs176832	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs176890	0.89[CEU][hapmap]
rs1779073	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1854562	0.89[CEU][hapmap]
rs200907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs200909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs200913	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs200914	0.81[EUR][1000 genomes]
rs200941	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs200944	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap]
rs2021651	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2178958	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2293962	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2472153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2472159	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2472160	0.88[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs2474542	0.84[ASN][1000 genomes]
rs2474545	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2474553	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2480521	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2489166	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504137	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505218	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2738221	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2753883	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7088655	0.89[CEU][hapmap]
rs766362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9418311	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1051121	chr10:38155991-38426204	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv540565	chr10:38155991-38426204	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv1052703	chr10:38174640-38266472	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv534122	chr10:38240258-38356008	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38257400-38265000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:38263800-38264800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr10:38264000-38264800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr10:38264000-38264800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
5	chr10:38264000-38264800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr10:38264000-38264800	Flanking Active TSS	K562	blood
7	chr10:38264000-38265000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr10:38264000-38265000	Active TSS	Brain Germinal Matrix	brain
9	chr10:38264000-38265800	Active TSS	Fetal Brain Female	brain
10	chr10:38264000-38266200	Active TSS	NHLF	lung
11	chr10:38264200-38264800	Flanking Active TSS	Fetal Lung	lung
12	chr10:38264200-38264800	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr10:38264200-38265000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr10:38264200-38265000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr10:38264200-38265000	Active TSS	Right Atrium	heart
16	chr10:38264200-38265000	Flanking Active TSS	Dnd41	blood
17	chr10:38264200-38265000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr10:38264200-38265200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr10:38264200-38265800	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr10:38264200-38265800	Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr10:38264200-38266000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr10:38264200-38266200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr10:38264200-38266200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr10:38264200-38266200	Active TSS	Brain Angular Gyrus	brain
25	chr10:38264200-38266200	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr10:38264200-38266200	Active TSS	HepG2	liver
27	chr10:38264200-38266400	Active TSS	A549	lung
28	chr10:38264400-38264800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr10:38264400-38264800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr10:38264400-38264800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr10:38264400-38264800	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr10:38264400-38264800	Flanking Active TSS	Brain Substantia Nigra	brain
33	chr10:38264400-38264800	Flanking Active TSS	Colon Smooth Muscle	Colon
34	chr10:38264400-38264800	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr10:38264400-38264800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr10:38264400-38264800	Flanking Active TSS	Fetal Brain Male	brain
37	chr10:38264400-38264800	Flanking Active TSS	Fetal Intestine Small	intestine
38	chr10:38264400-38264800	Flanking Active TSS	Fetal Muscle Leg	muscle
39	chr10:38264400-38264800	Enhancers	Placenta Amnion	Placenta Amnion
40	chr10:38264400-38264800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr10:38264400-38264800	Flanking Active TSS	GM12878-XiMat	blood
42	chr10:38264400-38264800	Flanking Active TSS	HMEC	breast
43	chr10:38264400-38264800	Flanking Active TSS	NHEK	skin
44	chr10:38264400-38265000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr10:38264400-38265000	Flanking Active TSS	Primary B cells from peripheral blood	blood
46	chr10:38264400-38265000	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr10:38264400-38265000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr10:38264400-38265000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr10:38264400-38265000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr10:38264400-38265000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links