Variant report

Variant	rs41690
Chromosome Location	chr7:120634383-120634384
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120633517..120635365-chr7:120747821..120749395,2	K562	blood:
2	chr7:120621518..120649031-chr7:120712706..120728931,108	K562	blood:
3	chr7:120624020..120645873-chr7:120713358..120727138,77	K562	blood:

Variant related genes	Relation type
ENSG00000212628	Chromatin interaction
ENSG00000106034	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10245939	0.82[AFR][1000 genomes]
rs10252911	0.85[CHB][hapmap];0.80[CHD][hapmap]
rs10272601	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs10277935	0.86[ASW][hapmap];0.97[LWK][hapmap];0.84[MKK][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs10464522	0.81[ASN][1000 genomes]
rs10953922	0.81[ASN][1000 genomes]
rs10953923	0.80[ASW][hapmap];0.97[LWK][hapmap];0.84[MKK][hapmap];0.90[YRI][hapmap]
rs1557857	0.82[ASN][1000 genomes]
rs1859316	0.85[CHB][hapmap]
rs1859318	0.82[ASN][1000 genomes]
rs1859319	0.82[ASN][1000 genomes]
rs2058501	0.80[ASW][hapmap];0.84[LWK][hapmap];0.83[MKK][hapmap]
rs2074577	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2107276	0.85[CHB][hapmap]
rs2244863	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244865	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2248890	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs2525705	0.82[ASN][1000 genomes]
rs2525709	0.81[ASN][1000 genomes]
rs2525712	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525713	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525719	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525729	0.89[ASN][1000 genomes]
rs2525730	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525736	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2525737	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525741	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2525743	0.81[ASN][1000 genomes]
rs2721341	0.93[ASW][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.83[LWK][hapmap];0.81[ASN][1000 genomes]
rs2721354	0.93[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2721358	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2721363	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721365	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721367	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721372	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757556	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs3779386	0.85[CHB][hapmap]
rs3823859	0.86[ASW][hapmap]
rs41688	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41689	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6466761	0.86[ASW][hapmap]
rs6466762	0.86[ASW][hapmap]
rs6944789	0.80[ASW][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap]
rs6949989	0.86[ASW][hapmap];0.97[LWK][hapmap];0.82[MKK][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs6958635	0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs6960415	0.86[AFR][1000 genomes]
rs6964344	0.89[CHB][hapmap];0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs6971854	0.85[CHB][hapmap]
rs6979247	0.85[CHB][hapmap]
rs745167	0.81[ASN][1000 genomes]
rs7776721	0.85[CHB][hapmap]
rs7781985	0.86[ASW][hapmap]
rs7782552	0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs996903	0.80[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831114	chr7:120595624-120804510	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv608327	chr7:120633006-120873078	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41690	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120629600-120635800	Weak transcription	Primary B cells from cord blood	blood
2	chr7:120630000-120636400	Weak transcription	HMEC	breast
3	chr7:120630200-120636200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:120630200-120636200	Weak transcription	Placenta	Placenta
5	chr7:120631200-120640400	Weak transcription	Brain Anterior Caudate	brain
6	chr7:120631400-120636200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr7:120632000-120634800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr7:120632000-120636400	Weak transcription	Hela-S3	cervix
9	chr7:120632200-120636600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:120632400-120641400	Transcr. at gene 5' and 3'	K562	blood
11	chr7:120632600-120634600	Weak transcription	Fetal Heart	heart
12	chr7:120632600-120635000	Enhancers	Rectal Smooth Muscle	rectum
13	chr7:120632800-120634400	Enhancers	Fetal Kidney	kidney
14	chr7:120633000-120634600	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr7:120633000-120636600	Weak transcription	HSMMtube	muscle
16	chr7:120633000-120636800	Enhancers	Liver	Liver
17	chr7:120633000-120636800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr7:120633200-120634600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr7:120633200-120634800	Enhancers	Osteobl	bone
20	chr7:120633200-120636400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr7:120633400-120635200	Enhancers	Fetal Stomach	stomach
22	chr7:120633600-120635400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr7:120633600-120636200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr7:120633600-120636200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr7:120633600-120636200	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr7:120633600-120636600	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr7:120633600-120636800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr7:120634000-120634600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:120634000-120635200	Weak transcription	Colon Smooth Muscle	Colon
30	chr7:120634000-120636200	Weak transcription	Brain Hippocampus Middle	brain
31	chr7:120634000-120636400	Weak transcription	Stomach Mucosa	stomach
32	chr7:120634000-120637400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr7:120634200-120634400	Enhancers	Fetal Brain Male	brain
34	chr7:120634200-120634400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr7:120634200-120634600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr7:120634200-120634600	Active TSS	Ovary	ovary
37	chr7:120634200-120634600	Weak transcription	Right Atrium	heart
38	chr7:120634200-120634600	Weak transcription	Right Ventricle	heart
39	chr7:120634200-120634600	Enhancers	NHDF-Ad	bronchial
40	chr7:120634200-120634800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr7:120634200-120634800	Active TSS	Stomach Smooth Muscle	stomach
42	chr7:120634200-120634800	Active TSS	NHLF	lung
43	chr7:120634200-120635000	Active TSS	Aorta	Aorta
44	chr7:120634200-120635000	Enhancers	Small Intestine	intestine
45	chr7:120634200-120635400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
46	chr7:120634200-120635600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr7:120634200-120635800	Strong transcription	HSMM	muscle
48	chr7:120634200-120636000	Weak transcription	Left Ventricle	heart
49	chr7:120634200-120636200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr7:120634200-120636200	Enhancers	Adipose Nuclei	Adipose

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