Variant report

Variant	rs7042852
Chromosome Location	chr9:101902827-101902828
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:101762134..101763385-chr9:101902694..101903814,11	K562	blood:
2	chr9:101866386..101868901-chr9:101901317..101903071,2	MCF-7	breast:
3	chr9:101622854..101623401-chr9:101902748..101903437,2	K562	blood:
4	chr9:101610517..101611394-chr9:101902660..101903289,2	MCF-7	breast:
5	chr9:101898800..101901227-chr9:101901633..101903156,2	K562	blood:
6	chr9:101901991..101903988-chr9:101906296..101908227,2	MCF-7	breast:
7	chr9:101610078..101611460-chr9:101902663..101903721,8	MCF-7	breast:
8	chr9:101751301..101751815-chr9:101902700..101903663,2	MCF-7	breast:
9	chr9:101898521..101900717-chr9:101901631..101904454,3	K562	blood:
10	chr9:101864987..101867823-chr9:101901500..101903919,2	K562	blood:
11	chr9:101737038..101737838-chr9:101902687..101903642,3	K562	blood:
12	chr9:101610575..101611904-chr9:101902666..101903641,7	K562	blood:
13	chr9:101762428..101763408-chr9:101902234..101903630,9	MCF-7	breast:
14	chr9:101762444..101763486-chr9:101902217..101903969,25	MCF-7	breast:
15	chr9:101760854..101761829-chr9:101902660..101903198,2	MCF-7	breast:
16	chr9:101608345..101611118-chr9:101900740..101903316,2	MCF-7	breast:
17	chr9:101865858..101869567-chr9:101901452..101906002,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000119514	Chromatin interaction
ENSG00000267026	Chromatin interaction
ENSG00000106799	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1013186	0.94[CEU][hapmap]
rs10283455	0.94[CEU][hapmap]
rs10448292	0.87[EUR][1000 genomes]
rs10733708	0.82[ASN][1000 genomes]
rs10733709	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10739778	0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs10739779	0.94[CEU][hapmap]
rs10760668	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10760669	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10760670	0.89[CEU][hapmap];0.90[CHD][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10760671	0.94[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10760672	0.94[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs10760673	0.94[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10760674	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819635	0.82[CHD][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.84[YRI][hapmap]
rs10819636	0.90[ASN][1000 genomes]
rs10819638	0.94[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10819639	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10819640	0.91[CHB][hapmap];0.88[CHD][hapmap];0.89[ASN][1000 genomes]
rs10988706	0.94[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10988709	0.91[CHB][hapmap];0.90[ASN][1000 genomes]
rs10988715	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs10988716	0.94[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10988717	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs10988723	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11568752	0.91[CHB][hapmap];0.90[ASN][1000 genomes]
rs11568753	0.95[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs11568770	1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs11568778	1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs12345675	0.95[EUR][1000 genomes]
rs12346650	0.87[CHB][hapmap];0.83[CHD][hapmap];0.92[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap]
rs12685571	0.91[CHB][hapmap];0.90[ASN][1000 genomes]
rs1571589	0.89[CEU][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1571590	0.94[CEU][hapmap]
rs1590	0.87[ASW][hapmap];0.95[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1626340	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1699413	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1888225	0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[ASN][1000 genomes]
rs1973518	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2026811	0.89[CEU][hapmap];0.90[CHD][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs334348	0.87[ASW][hapmap];0.95[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs334349	0.93[ASW][hapmap];0.95[CEU][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs334351	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs334353	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs334354	0.94[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs334355	0.89[CEU][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs334356	0.94[CEU][hapmap]
rs334357	0.94[CEU][hapmap]
rs334358	0.94[CEU][hapmap]
rs334362	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs334363	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs334364	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs334366	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs334367	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs334368	0.88[EUR][1000 genomes]
rs334369	0.89[EUR][1000 genomes]
rs334370	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs367568	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs3739798	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[ASN][1000 genomes]
rs383496	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs401186	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs420549	0.94[CEU][hapmap]
rs44466	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs478061	0.89[EUR][1000 genomes]
rs597457	0.94[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6478972	0.89[CEU][hapmap];0.90[CHD][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6478973	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7031302	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7031309	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7041311	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7043624	0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7874221	0.94[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs868	0.94[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893619	chr9:101835165-101936231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv831666	chr9:101874985-102018690	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv1792736	chr9:101891126-101909372	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7042852	TGFBR1	cis	cerebellum	SCAN
rs7042852	LOC286359	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101870000-101908600	Weak transcription	Brain Germinal Matrix	brain
2	chr9:101876600-101904200	Weak transcription	Liver	Liver
3	chr9:101878800-101903200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr9:101882200-101903000	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:101888200-101907000	Weak transcription	HepG2	liver
6	chr9:101889400-101904000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:101889800-101904400	Weak transcription	Lung	lung
8	chr9:101890000-101914200	Weak transcription	Pancreas	Pancrea
9	chr9:101890200-101904800	Weak transcription	Fetal Intestine Large	intestine
10	chr9:101890200-101907600	Weak transcription	Gastric	stomach
11	chr9:101890400-101908400	Weak transcription	Hela-S3	cervix
12	chr9:101890600-101907000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr9:101890600-101908800	Weak transcription	Right Ventricle	heart
14	chr9:101890800-101903600	Weak transcription	Right Atrium	heart
15	chr9:101891400-101903600	Weak transcription	Dnd41	blood
16	chr9:101892600-101914200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:101892800-101905800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:101892800-101921000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:101893000-101904200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr9:101894200-101906800	Weak transcription	Fetal Kidney	kidney
21	chr9:101894200-101907600	Weak transcription	HUVEC	blood vessel
22	chr9:101895000-101907200	Weak transcription	Spleen	Spleen
23	chr9:101895000-101914200	Weak transcription	Esophagus	oesophagus
24	chr9:101895200-101903800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr9:101895400-101904200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr9:101897600-101907400	Weak transcription	HMEC	breast
27	chr9:101897600-101913400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr9:101897600-101915400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:101897800-101903800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:101897800-101906800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:101898000-101903200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr9:101898000-101904800	Weak transcription	Fetal Brain Female	brain
33	chr9:101898000-101905400	Weak transcription	NH-A	brain
34	chr9:101898000-101907000	Weak transcription	NHLF	lung
35	chr9:101898000-101907200	Weak transcription	Small Intestine	intestine
36	chr9:101898000-101907400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:101898000-101907400	Weak transcription	Brain Angular Gyrus	brain
38	chr9:101898000-101907400	Weak transcription	Brain Hippocampus Middle	brain
39	chr9:101898000-101907400	Weak transcription	Brain Substantia Nigra	brain
40	chr9:101898000-101912200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr9:101898000-101919400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr9:101898200-101906000	Weak transcription	Fetal Brain Male	brain
43	chr9:101898400-101903200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr9:101898400-101905000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr9:101899000-101906800	Weak transcription	Fetal Thymus	thymus
46	chr9:101899000-101913000	Strong transcription	HSMM	muscle
47	chr9:101899400-101908000	Weak transcription	Colonic Mucosa	Colon
48	chr9:101899400-101913000	Weak transcription	Thymus	Thymus
49	chr9:101900000-101905800	Weak transcription	GM12878-XiMat	blood
50	chr9:101900200-101903200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood

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