Variant report

Variant	rs313829
Chromosome Location	chr7:65552497-65552498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:65550364..65553168-chr7:65578691..65580268,2	K562	blood:
2	chr7:65550364..65554176-chr7:65578691..65580881,4	K562	blood:
3	chr7:65540457..65542538-chr7:65550059..65552910,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126522	Chromatin interaction
ENSG00000241258	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10256544	0.83[YRI][hapmap]
rs10282433	0.83[YRI][hapmap]
rs10950026	0.87[CEU][hapmap]
rs10950029	0.87[CEU][hapmap];0.85[GIH][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap]
rs1129531	0.83[YRI][hapmap]
rs1167390	0.83[YRI][hapmap]
rs1167406	0.82[YRI][hapmap]
rs11760844	0.83[YRI][hapmap]
rs11769702	0.83[CEU][hapmap];0.86[TSI][hapmap]
rs12537823	0.83[YRI][hapmap]
rs13245728	0.83[YRI][hapmap]
rs1547529	0.87[CEU][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap]
rs160641	0.87[CEU][hapmap];0.85[GIH][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap]
rs160645	0.83[AFR][1000 genomes]
rs160647	0.86[AFR][1000 genomes]
rs17138149	0.87[CEU][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap]
rs1976200	0.83[YRI][hapmap]
rs2249458	0.83[YRI][hapmap]
rs2420456	0.87[CEU][hapmap];0.89[TSI][hapmap]
rs313818	0.94[YRI][hapmap]
rs313828	0.84[AFR][1000 genomes]
rs313830	0.87[CEU][hapmap];0.83[GIH][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs316305	0.87[CEU][hapmap];0.85[GIH][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap]
rs316306	0.87[CEU][hapmap];0.85[GIH][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap]
rs316323	0.87[CEU][hapmap];0.85[GIH][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap]
rs316324	0.87[CEU][hapmap];0.85[GIH][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap]
rs316328	0.91[CEU][hapmap];0.85[GIH][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap]
rs400767	0.81[AFR][1000 genomes]
rs4149461	0.83[YRI][hapmap]
rs4718330	0.83[YRI][hapmap]
rs6460269	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6460281	0.87[CEU][hapmap];0.89[TSI][hapmap]
rs6971509	0.84[ASW][hapmap];0.83[YRI][hapmap]
rs6979636	0.87[CEU][hapmap];0.86[TSI][hapmap]
rs697970	0.83[YRI][hapmap]
rs7783889	0.87[CEU][hapmap];0.88[YRI][hapmap]
rs7811214	0.87[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs880166	0.82[YRI][hapmap]
rs908915	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv888325	chr7:65474919-65575893	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv984546	chr7:65531382-65556631	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers 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	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs313829	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs313829	GS1-124K5.4	cis	Stomach	GTEx
rs313829	RP4-756H11.3	cis	Artery Tibial	GTEx
rs313829	RABGEF1	cis	cerebellum	SCAN
rs313829	RABGEF1	cis	parietal	SCAN
rs313829	GS1-124K5.4	cis	Whole Blood	GTEx
rs313829	RP4-756H11.3	cis	Thyroid	GTEx
rs313829	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs313829	RP11-479O9.2	cis	Thyroid	GTEx
rs313829	GUSB	cis	parietal	SCAN
rs313829	KCTD7	cis	parietal	SCAN
rs313829	ZNF273	cis	cerebellum	SCAN
rs313829	LOC168474	cis	cerebellum	SCAN
rs313829	ZNF117	cis	cerebellum	SCAN
rs313829	RP4-756H11.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65541600-65565000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:65541800-65554200	Weak transcription	HSMMtube	muscle
3	chr7:65541800-65556800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:65541800-65564600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:65541800-65564600	Weak transcription	Fetal Brain Female	brain
6	chr7:65541800-65564800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr7:65542000-65553400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:65542000-65553600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr7:65542000-65554400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:65542000-65559600	Weak transcription	Psoas Muscle	Psoas
11	chr7:65542000-65564600	Weak transcription	Primary B cells from cord blood	blood
12	chr7:65542000-65564800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr7:65542000-65564800	Weak transcription	Aorta	Aorta
14	chr7:65542000-65564800	Weak transcription	HSMM	muscle
15	chr7:65542200-65556000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr7:65542200-65564600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr7:65542200-65564600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:65542200-65564600	Weak transcription	Brain Angular Gyrus	brain
19	chr7:65542200-65564600	Weak transcription	Fetal Kidney	kidney
20	chr7:65542200-65564600	Weak transcription	NH-A	brain
21	chr7:65542200-65564800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr7:65542400-65556200	Weak transcription	Osteobl	bone
23	chr7:65542400-65564400	Weak transcription	Hela-S3	cervix
24	chr7:65542800-65560600	Strong transcription	Fetal Stomach	stomach
25	chr7:65543000-65564600	Weak transcription	NHDF-Ad	bronchial
26	chr7:65543200-65554600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr7:65543200-65564400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr7:65543400-65558600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:65543400-65558600	Weak transcription	Small Intestine	intestine
30	chr7:65543400-65559200	Strong transcription	Fetal Intestine Large	intestine
31	chr7:65543600-65561400	Strong transcription	Fetal Intestine Small	intestine
32	chr7:65544000-65553000	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr7:65544200-65554000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr7:65545600-65553200	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr7:65545600-65554800	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr7:65545600-65558200	Strong transcription	Lung	lung
37	chr7:65545800-65554400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr7:65546000-65552800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr7:65546000-65555400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr7:65546200-65560600	Strong transcription	Liver	Liver
41	chr7:65546400-65554400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr7:65546400-65559000	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr7:65546600-65552800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr7:65546600-65553800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr7:65546800-65554800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr7:65547000-65553000	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr7:65547200-65552600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:65548000-65555600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr7:65548000-65564600	Weak transcription	GM12878-XiMat	blood
50	chr7:65548200-65564600	Weak transcription	Brain Substantia Nigra	brain

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