Variant report

Variant	rs10011292
Chromosome Location	chr4:186648646-186648647
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:186642780..186645447-chr4:186647072..186650843,3	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10015763	0.84[EUR][1000 genomes]
rs10016122	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs10017672	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10017940	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10018379	0.94[ASN][1000 genomes]
rs10019263	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs11132336	0.87[EUR][1000 genomes]
rs11132337	0.87[EUR][1000 genomes]
rs11132338	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11132339	0.88[EUR][1000 genomes]
rs1124024	0.88[CEU][hapmap]
rs11725010	0.87[EUR][1000 genomes]
rs11733264	0.87[EUR][1000 genomes]
rs11932587	0.87[EUR][1000 genomes]
rs11937510	0.87[EUR][1000 genomes]
rs11941721	0.87[EUR][1000 genomes]
rs12643220	0.84[EUR][1000 genomes]
rs12649216	0.84[EUR][1000 genomes]
rs13119888	0.89[CEU][hapmap]
rs1540711	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1542847	0.82[EUR][1000 genomes]
rs1566350	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs2030143	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs2030144	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2047499	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4376189	0.82[JPT][hapmap]
rs4407549	0.88[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4640708	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4861676	0.90[EUR][1000 genomes]
rs4862561	0.88[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs4862565	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4862566	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6552917	0.80[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs6812761	0.87[EUR][1000 genomes]
rs6820044	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs6825114	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs6825669	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs6826210	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs6836237	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6837079	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7340885	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7688359	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7694063	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696530	0.85[EUR][1000 genomes]
rs950590	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432684	chr4:186412851-186742851	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1028146	chr4:186503899-187338335	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1020731	chr4:186512433-186724031	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1023917	chr4:186533075-186997806	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer 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	7 gene(s)	inside rSNPs	diseases
5	nsv537420	chr4:186533075-186997806	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv830171	chr4:186610113-186789271	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1023412	chr4:186613289-186707428	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv537421	chr4:186613289-186707428	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv427702	chr4:186618031-186782377	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:186622000-186651800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:186630000-186651600	Weak transcription	HSMM	muscle
3	chr4:186634400-186651800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:186638600-186651600	Weak transcription	Psoas Muscle	Psoas
5	chr4:186639000-186651000	Enhancers	Fetal Heart	heart
6	chr4:186640800-186653600	Weak transcription	Fetal Intestine Large	intestine
7	chr4:186641400-186651600	Weak transcription	Right Ventricle	heart
8	chr4:186642200-186651600	Weak transcription	Spleen	Spleen
9	chr4:186642800-186651600	Weak transcription	Lung	lung
10	chr4:186642800-186657800	Weak transcription	Gastric	stomach
11	chr4:186643000-186649200	Weak transcription	Pancreas	Pancrea
12	chr4:186643000-186651600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:186643000-186654000	Weak transcription	Fetal Intestine Small	intestine
14	chr4:186643400-186651800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:186643600-186650400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:186643800-186650600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:186643800-186657800	Weak transcription	Fetal Brain Female	brain
18	chr4:186644800-186651800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:186645200-186651600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr4:186645400-186650000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:186645400-186651800	Weak transcription	Stomach Mucosa	stomach
22	chr4:186645600-186651600	Weak transcription	GM12878-XiMat	blood
23	chr4:186645800-186649600	Weak transcription	HUVEC	blood vessel
24	chr4:186645800-186651600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:186645800-186651600	Weak transcription	Right Atrium	heart
26	chr4:186645800-186651800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:186646000-186649200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:186646000-186649200	Weak transcription	Left Ventricle	heart
29	chr4:186646000-186651600	Weak transcription	Ovary	ovary
30	chr4:186646400-186650000	Enhancers	Liver	Liver
31	chr4:186646800-186653600	Weak transcription	HepG2	liver
32	chr4:186647000-186651000	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr4:186647800-186649000	Enhancers	Colon Smooth Muscle	Colon
34	chr4:186647800-186649400	Weak transcription	Placenta	Placenta
35	chr4:186648000-186648800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:186648000-186649200	Enhancers	Fetal Kidney	kidney
37	chr4:186648000-186649400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:186648000-186650800	Enhancers	Aorta	Aorta
39	chr4:186648400-186648800	Weak transcription	Brain Anterior Caudate	brain
40	chr4:186648400-186649200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:186648400-186649400	Weak transcription	HSMMtube	muscle
42	chr4:186648400-186650200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr4:186648400-186650600	Weak transcription	Fetal Muscle Leg	muscle
44	chr4:186648400-186651200	Weak transcription	Fetal Stomach	stomach
45	chr4:186648400-186658800	Weak transcription	Brain Germinal Matrix	brain
46	chr4:186648600-186650200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:186648600-186650200	Weak transcription	NHDF-Ad	bronchial
48	chr4:186648600-186651600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:186648600-186651600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr4:186648600-186651800	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links