Variant report

Variant	rs2299439
Chromosome Location	chr7:116416010-116416011
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr7:116415630-116418499	SK-N-SH	brain:	n/a	chr7:116416724-116416731 chr7:116416722-116416732
2	SRF	chr7:116415992-116418130	HCT-116	colon:	n/a	chr7:116416250-116416267 chr7:116416251-116416266 chr7:116416252-116416263

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:116411338..116414337-chr7:116414507..116416742,3	K562	blood:

Variant related genes	Relation type
MET	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10435378	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1049618	1.00[YRI][hapmap]
rs168686	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16945	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs183642	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs187437	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs193688	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]
rs2023748	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237717	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2402118	0.92[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs35759345	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38848	0.82[JPT][hapmap]
rs38851	0.81[JPT][hapmap]
rs38854	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs38859	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs39748	0.82[JPT][hapmap]
rs41735	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41736	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41737	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41738	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41739	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41743	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41744	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41746	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41747	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41748	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41749	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41774	1.00[YRI][hapmap]
rs41775	1.00[YRI][hapmap]
rs42229	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs42336	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs42374	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4730762	1.00[YRI][hapmap]
rs6566	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6947629	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6951311	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6978135	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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
rs2299439	KCND2	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116375000-116418400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr7:116378800-116422200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:116381600-116418600	Weak transcription	Aorta	Aorta
4	chr7:116388400-116416200	Weak transcription	Fetal Stomach	stomach
5	chr7:116393000-116419000	Weak transcription	Left Ventricle	heart
6	chr7:116403600-116416400	Weak transcription	Brain Substantia Nigra	brain
7	chr7:116404000-116420400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:116406400-116421000	Weak transcription	Lung	lung
9	chr7:116407200-116419400	Weak transcription	Gastric	stomach
10	chr7:116408600-116419000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:116409400-116416200	Genic enhancers	HUVEC	blood vessel
12	chr7:116410000-116422200	Weak transcription	Adipose Nuclei	Adipose
13	chr7:116410200-116416600	Weak transcription	HSMMtube	muscle
14	chr7:116410200-116420400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:116410600-116416400	Genic enhancers	NHEK	skin
16	chr7:116411000-116416200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr7:116411000-116418000	Weak transcription	Placenta	Placenta
18	chr7:116411400-116418200	Weak transcription	Psoas Muscle	Psoas
19	chr7:116411600-116416200	Weak transcription	Colon Smooth Muscle	Colon
20	chr7:116412800-116416200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr7:116412800-116417400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr7:116413400-116420000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:116413400-116424000	Weak transcription	Colonic Mucosa	Colon
24	chr7:116413600-116416200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:116413600-116416200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr7:116413600-116416200	Weak transcription	Pancreas	Pancrea
27	chr7:116413600-116416200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr7:116413600-116419200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr7:116413800-116416200	Weak transcription	Fetal Intestine Large	intestine
30	chr7:116413800-116416200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr7:116413800-116416200	Strong transcription	Hela-S3	cervix
32	chr7:116413800-116418200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr7:116414000-116416200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr7:116414000-116416200	Weak transcription	HepG2	liver
35	chr7:116414200-116416200	Weak transcription	Liver	Liver
36	chr7:116414400-116416200	Weak transcription	NHLF	lung
37	chr7:116414400-116416600	Weak transcription	Brain Hippocampus Middle	brain
38	chr7:116414400-116416800	Weak transcription	Brain Anterior Caudate	brain
39	chr7:116415000-116416600	Genic enhancers	Muscle Satellite Cultured Cells	--
40	chr7:116415200-116418600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr7:116415200-116421200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr7:116415400-116416600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr7:116415400-116418200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr7:116415600-116416200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr7:116415800-116416200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr7:116415800-116416200	Genic enhancers	HMEC	breast
47	chr7:116415800-116416200	Weak transcription	HSMM	muscle
48	chr7:116415800-116416600	Enhancers	Fetal Kidney	kidney
49	chr7:116415800-116416800	Enhancers	Fetal Intestine Small	intestine
50	chr7:116415800-116418200	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links