Variant report

Variant	rs7905676
Chromosome Location	chr10:43881075-43881076
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43855647..43857752-chr10:43878006..43881075,3	MCF-7	breast:
2	chr10:43868177..43875753-chr10:43880229..43888906,15	MCF-7	breast:
3	chr10:43858007..43859575-chr10:43879795..43881644,2	MCF-7	breast:
4	chr10:43879008..43883052-chr10:43949060..43952010,4	K562	blood:
5	chr10:43879370..43881344-chr10:43930901..43933311,2	MCF-7	breast:
6	chr10:43858972..43861250-chr10:43879046..43881690,2	K562	blood:

Variant related genes	Relation type
ENSG00000150201	Chromatin interaction
ENSG00000243660	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10409	0.90[JPT][hapmap]
rs10732897	0.89[AMR][1000 genomes]
rs10793430	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10793431	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs10899794	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10899797	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10899803	0.90[JPT][hapmap]
rs10899807	0.90[JPT][hapmap]
rs1112959	0.84[JPT][hapmap]
rs11238526	0.95[ASN][1000 genomes]
rs11238532	0.90[JPT][hapmap]
rs11238536	0.90[JPT][hapmap]
rs11238542	0.81[AMR][1000 genomes]
rs11238553	0.90[JPT][hapmap]
rs1126487	0.84[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1126709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12220230	0.90[JPT][hapmap]
rs12240317	0.84[JPT][hapmap]
rs12245391	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs12250140	0.90[JPT][hapmap]
rs12257917	0.99[ASN][1000 genomes]
rs12260474	0.84[JPT][hapmap]
rs13376803	0.89[JPT][hapmap]
rs1416226	0.85[JPT][hapmap]
rs2066044	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2247979	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2247981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2248335	0.86[JPT][hapmap]
rs2250444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2252783	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2252785	0.85[JPT][hapmap]
rs2252800	0.99[ASN][1000 genomes]
rs2255967	0.99[ASN][1000 genomes]
rs2256613	0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2259045	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2260200	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2261636	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2265886	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2265887	0.89[ASN][1000 genomes]
rs2265952	0.96[ASN][1000 genomes]
rs2265953	0.85[ASN][1000 genomes]
rs2460558	0.88[ASN][1000 genomes]
rs2492404	0.84[ASN][1000 genomes]
rs2492405	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2492407	0.93[ASN][1000 genomes]
rs2493648	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2819021	0.84[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes]
rs2819032	0.99[ASN][1000 genomes]
rs2819034	0.97[ASN][1000 genomes]
rs2946992	0.88[ASN][1000 genomes]
rs2999286	0.86[ASN][1000 genomes]
rs3000700	0.95[ASN][1000 genomes]
rs3000708	0.81[AMR][1000 genomes]
rs3750890	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs4597022	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs4948726	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs56059584	0.99[ASN][1000 genomes]
rs60739384	0.88[ASN][1000 genomes]
rs61859002	0.92[ASN][1000 genomes]
rs7070029	0.94[ASN][1000 genomes]
rs7070769	0.83[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7088430	0.91[ASN][1000 genomes]
rs7914140	0.85[JPT][hapmap]
rs7918726	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7920539	0.83[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9422371	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7905676	HNRNPF	cis	brain	BrainEAC
rs7905676	HNRNPF	cis	inferior olivary nucleus	BrainEAC

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43858600-43891000	Weak transcription	Right Atrium	heart
2	chr10:43869200-43882000	Weak transcription	Left Ventricle	heart
3	chr10:43870000-43881200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr10:43870000-43882000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr10:43870200-43882000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr10:43870200-43882000	Weak transcription	Brain Substantia Nigra	brain
7	chr10:43870400-43881600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr10:43870400-43882000	Weak transcription	Brain Angular Gyrus	brain
9	chr10:43871200-43881600	Weak transcription	Brain Hippocampus Middle	brain
10	chr10:43873200-43881200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr10:43873200-43890200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr10:43873400-43881200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr10:43873400-43881400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr10:43873400-43881800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr10:43873400-43882000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:43873400-43891000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr10:43873800-43882000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr10:43873800-43882000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:43874400-43882400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr10:43876000-43881800	Weak transcription	Colon Smooth Muscle	Colon
21	chr10:43877200-43882000	Weak transcription	Psoas Muscle	Psoas
22	chr10:43877400-43882000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr10:43877600-43881800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr10:43878000-43881600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr10:43878400-43881600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr10:43878600-43882600	Weak transcription	Fetal Brain Male	brain
27	chr10:43878800-43882200	Weak transcription	Fetal Kidney	kidney
28	chr10:43879000-43882000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr10:43879200-43881600	Weak transcription	Fetal Lung	lung
30	chr10:43879200-43881600	Weak transcription	NHDF-Ad	bronchial
31	chr10:43879200-43882000	Weak transcription	Aorta	Aorta
32	chr10:43879200-43882000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr10:43879200-43889800	Strong transcription	Brain Germinal Matrix	brain
34	chr10:43879400-43881800	Weak transcription	K562	blood
35	chr10:43879400-43882000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr10:43879400-43882000	Weak transcription	Fetal Intestine Small	intestine
37	chr10:43879400-43882000	Weak transcription	Ovary	ovary
38	chr10:43879400-43889400	Strong transcription	Fetal Brain Female	brain
39	chr10:43879600-43881200	Enhancers	Fetal Heart	heart
40	chr10:43879600-43881200	Weak transcription	HepG2	liver
41	chr10:43879600-43882000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr10:43879600-43882600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr10:43879600-43885800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr10:43879600-43889400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr10:43879800-43883000	Strong transcription	Primary B cells from cord blood	blood
46	chr10:43879800-43883000	Strong transcription	Primary T cells from cord blood	blood
47	chr10:43879800-43889400	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr10:43879800-43890600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr10:43880000-43882000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr10:43880000-43882000	Strong transcription	Fetal Thymus	thymus

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