Variant report

Variant	rs193688
Chromosome Location	chr7:116433527-116433528
allele	C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	7:115924626-115929516..7:116433150-116434729	H1-hESC	embryonic stem cell:	embryo
2	7:115890993-115892266..7:116433150-116434729	GM12878	blood:
3	chr7:116426630..116429182-chr7:116432442..116434146,2	MCF-7	breast:
4	chr7:116431432..116434327-chr7:116437378..116438880,2	MCF-7	breast:
5	chr7:116420793..116424066-chr7:116430514..116433680,3	MCF-7	breast:
6	7:115861595-115870968..7:116433150-116434729	GM12878	blood:
7	7:116433150-116434729..7:116957165-116964911	H1-hESC	embryonic stem cell:	embryo
8	7:115847372-115857098..7:116433150-116434729	GM12878	blood:

No data

Variant related genes	Relation type
ENSG00000105971	Chromatin interaction
ENSG00000105989	Chromatin interaction
ENSG00000135269	Chromatin interaction
ENSG00000237870	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10435378	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1049618	1.00[YRI][hapmap]
rs11766819	0.80[GIH][hapmap]
rs168686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16945	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs183642	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs187437	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2023748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237717	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2299439	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2402118	0.84[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs35759345	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs38848	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs38851	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs38854	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs38859	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs39748	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs41735	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41736	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41737	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41738	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41744	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41747	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41748	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41749	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41774	1.00[YRI][hapmap]
rs41775	1.00[YRI][hapmap]
rs42229	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs42336	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42374	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4730762	1.00[YRI][hapmap]
rs6566	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6947629	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6951311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6978135	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964449	1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831107	chr7:116414734-116649466	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs193688	KCND2	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116418000-116437600	Weak transcription	Spleen	Spleen
2	chr7:116421800-116435800	Weak transcription	Aorta	Aorta
3	chr7:116421800-116444000	Weak transcription	Esophagus	oesophagus
4	chr7:116422000-116435800	Weak transcription	Placenta	Placenta
5	chr7:116423000-116439000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:116423000-116442600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:116423200-116435800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:116423200-116438000	Weak transcription	Adipose Nuclei	Adipose
9	chr7:116424000-116440800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:116424200-116440600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:116424200-116445400	Weak transcription	Left Ventricle	heart
12	chr7:116424400-116434400	Weak transcription	Hela-S3	cervix
13	chr7:116424600-116434400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr7:116425000-116440800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:116425800-116435600	Weak transcription	Fetal Stomach	stomach
16	chr7:116426200-116440800	Weak transcription	HSMMtube	muscle
17	chr7:116426400-116434400	Weak transcription	Fetal Muscle Leg	muscle
18	chr7:116427000-116440800	Weak transcription	NHDF-Ad	bronchial
19	chr7:116427200-116434600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr7:116427200-116437400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:116427400-116434600	Weak transcription	HUVEC	blood vessel
22	chr7:116427400-116440200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:116427400-116445200	Weak transcription	Pancreas	Pancrea
24	chr7:116427600-116435600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr7:116427800-116435600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr7:116427800-116435600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr7:116429000-116434000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr7:116429000-116436400	Weak transcription	HepG2	liver
29	chr7:116429200-116434000	Weak transcription	Stomach Mucosa	stomach
30	chr7:116429600-116434200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr7:116429600-116434200	Weak transcription	HSMM	muscle
32	chr7:116429600-116441200	Weak transcription	Fetal Lung	lung
33	chr7:116429800-116434400	Weak transcription	Liver	Liver
34	chr7:116430200-116435600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr7:116430200-116436000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr7:116430800-116435400	Weak transcription	Osteobl	bone
37	chr7:116430800-116435600	Weak transcription	HMEC	breast
38	chr7:116430800-116440000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr7:116431000-116434200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr7:116431000-116435800	Weak transcription	Psoas Muscle	Psoas
41	chr7:116432400-116439200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr7:116432800-116433600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr7:116432800-116434400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr7:116432800-116437200	Strong transcription	NHEK	skin
45	chr7:116433000-116434000	Strong transcription	A549	lung
46	chr7:116433200-116435800	Weak transcription	NH-A	brain
47	chr7:116433200-116436400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr7:116433200-116436800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr7:116433200-116442400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr7:116433200-116442600	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links