Variant report

Variant	rs12572339
Chromosome Location	chr10:5736575-5736576
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr10:5736510-5736948	GM12878	blood:	n/a	n/a
2	RUNX3	chr10:5736570-5736999	GM12878	blood:	n/a	n/a
3	CUX1	chr10:5736336-5736868	GM12878	blood:	n/a	n/a
4	POLR2A	chr10:5736447-5736589	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:5733731..5736743-chr10:5750015..5755601,4	MCF-7	breast:
2	chr10:5487726..5489985-chr10:5734513..5736734,2	K562	blood:
3	chr10:5724274..5728540-chr10:5734829..5741563,8	MCF-7	breast:
4	chr10:5735790..5738712-chr10:5931841..5933412,2	MCF-7	breast:
5	chr10:5702075..5704019-chr10:5735223..5736822,2	MCF-7	breast:
6	chr10:5487726..5489985-chr10:5734513..5736734,3	K562	blood:
7	chr10:5733787..5736575-chr10:5751182..5753712,2	MCF-7	breast:

No data

Variant related genes	Relation type
FAM208B	TF binding region
ENSG00000173848	Chromatin interaction
ENSG00000134452	Chromatin interaction
ENSG00000134461	Chromatin interaction
ENSG00000108021	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11254115	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11254828	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11254898	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12257412	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12571055	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2246268	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2275772	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2669133	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2669139	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2797490	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2797492	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2797497	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34404996	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3750636	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3793708	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3924378	0.81[ASN][1000 genomes]
rs57103262	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58502403	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59827083	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7089693	0.81[ASN][1000 genomes]
rs7096328	0.94[ASN][1000 genomes]
rs73610559	1.00[EUR][1000 genomes];0.98[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	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS 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	33 gene(s)	inside rSNPs	diseases
3	esv2758209	chr10:5637111-5804780	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	esv1796213	chr10:5716555-5766165	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv522415	chr10:5721653-5768493	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer 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 miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv8600	chr10:5733691-5736727	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5728800-5746800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr10:5734800-5763400	Weak transcription	HSMM	muscle
3	chr10:5735000-5736800	Enhancers	Small Intestine	intestine
4	chr10:5735200-5736600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr10:5735200-5736600	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr10:5735200-5736800	Enhancers	Primary B cells from peripheral blood	blood
7	chr10:5735200-5736800	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr10:5735200-5736800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr10:5735200-5736800	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr10:5735200-5737000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr10:5735200-5737000	Enhancers	Brain Substantia Nigra	brain
12	chr10:5735200-5737200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr10:5735200-5737400	Enhancers	Primary B cells from cord blood	blood
14	chr10:5735200-5737600	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr10:5735200-5737600	Weak transcription	Dnd41	blood
16	chr10:5735200-5737800	Weak transcription	Psoas Muscle	Psoas
17	chr10:5735200-5738800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr10:5735200-5739000	Weak transcription	Fetal Intestine Large	intestine
19	chr10:5735200-5739400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr10:5735200-5739400	Weak transcription	Lung	lung
21	chr10:5735200-5739400	Weak transcription	Pancreas	Pancrea
22	chr10:5735200-5739800	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr10:5735200-5743000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr10:5735200-5749000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr10:5735200-5750600	Weak transcription	Gastric	stomach
26	chr10:5735200-5767000	Weak transcription	Fetal Muscle Leg	muscle
27	chr10:5735400-5736600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr10:5735400-5736600	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr10:5735400-5736600	Enhancers	Brain Cingulate Gyrus	brain
30	chr10:5735400-5736600	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr10:5735400-5737000	Enhancers	Primary hematopoietic stem cells	blood
32	chr10:5735400-5737000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr10:5735400-5737000	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr10:5735400-5737000	Enhancers	Brain Hippocampus Middle	brain
35	chr10:5735400-5737200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr10:5735400-5737400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr10:5735400-5737800	Weak transcription	Left Ventricle	heart
38	chr10:5735400-5738000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr10:5735400-5738000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr10:5735400-5738200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr10:5735400-5738200	Weak transcription	Right Atrium	heart
42	chr10:5735400-5738400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr10:5735400-5738600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr10:5735400-5739200	Weak transcription	Fetal Heart	heart
45	chr10:5735400-5739200	Weak transcription	Fetal Intestine Small	intestine
46	chr10:5735400-5739400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr10:5735400-5739400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr10:5735400-5739400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr10:5735400-5739600	Weak transcription	Colonic Mucosa	Colon
50	chr10:5735400-5744800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links