Variant report

Variant	rs10435378
Chromosome Location	chr7:116425493-116425494
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:116308824..116313523-chr7:116420776..116428402,10	MCF-7	breast:
2	chr7:116422429..116424558-chr7:116424968..116427156,2	K562	blood:
3	chr7:116310897..116313625-chr7:116424372..116428199,3	MCF-7	breast:
4	chr7:116422162..116423929-chr7:116425324..116427156,2	K562	blood:

Variant related genes	Relation type
ENSG00000105976	Chromatin interaction

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

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

rs_ID	r²[population]
rs1049618	1.00[YRI][hapmap]
rs168686	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16945	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[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];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs183642	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs187437	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs193688	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]
rs2023748	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237717	0.96[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.98[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];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299439	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]
rs2402118	0.92[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs35759345	1.00[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38848	0.82[JPT][hapmap]
rs38851	0.81[JPT][hapmap]
rs38854	0.91[JPT][hapmap]
rs38859	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[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];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs39748	0.82[JPT][hapmap]
rs41735	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41736	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41737	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[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];0.98[ASN][1000 genomes]
rs41738	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41739	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41743	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41744	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41746	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41747	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41748	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41749	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41774	1.00[YRI][hapmap]
rs41775	1.00[YRI][hapmap]
rs42229	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs42336	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[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];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs42374	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4730762	1.00[YRI][hapmap]
rs6566	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[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];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6947629	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6951311	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6978135	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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
rs10435378	KCND2	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116418000-116437600	Weak transcription	Spleen	Spleen
2	chr7:116419600-116429200	Weak transcription	Fetal Brain Male	brain
3	chr7:116421400-116426600	Weak transcription	Right Ventricle	heart
4	chr7:116421800-116427000	Weak transcription	Gastric	stomach
5	chr7:116421800-116428400	Weak transcription	Lung	lung
6	chr7:116421800-116435800	Weak transcription	Aorta	Aorta
7	chr7:116421800-116444000	Weak transcription	Esophagus	oesophagus
8	chr7:116422000-116435800	Weak transcription	Placenta	Placenta
9	chr7:116422400-116426600	Weak transcription	Stomach Mucosa	stomach
10	chr7:116422800-116426400	Strong transcription	A549	lung
11	chr7:116423000-116425600	Strong transcription	Osteobl	bone
12	chr7:116423000-116426600	Weak transcription	NHDF-Ad	bronchial
13	chr7:116423000-116426800	Weak transcription	NHLF	lung
14	chr7:116423000-116427200	Weak transcription	Brain Substantia Nigra	brain
15	chr7:116423000-116428000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:116423000-116428600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr7:116423000-116431400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:116423000-116439000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr7:116423000-116442600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr7:116423200-116426400	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr7:116423200-116430800	Strong transcription	HMEC	breast
22	chr7:116423200-116431000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr7:116423200-116432200	Strong transcription	NHEK	skin
24	chr7:116423200-116435800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr7:116423200-116438000	Weak transcription	Adipose Nuclei	Adipose
26	chr7:116423400-116427000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr7:116423400-116432600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr7:116423600-116425600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr7:116423600-116425800	Strong transcription	Fetal Stomach	stomach
30	chr7:116423600-116426000	Strong transcription	NH-A	brain
31	chr7:116423600-116426600	Strong transcription	HSMM	muscle
32	chr7:116423600-116431000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr7:116423800-116425800	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr7:116423800-116426000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr7:116423800-116426200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr7:116423800-116427400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr7:116423800-116427800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr7:116424000-116425600	Weak transcription	HSMMtube	muscle
39	chr7:116424000-116426400	Strong transcription	Fetal Muscle Leg	muscle
40	chr7:116424000-116427000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr7:116424000-116428400	Weak transcription	Fetal Lung	lung
42	chr7:116424000-116440800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr7:116424200-116426000	Weak transcription	Brain Angular Gyrus	brain
44	chr7:116424200-116426000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr7:116424200-116426400	Weak transcription	HUVEC	blood vessel
46	chr7:116424200-116426800	Weak transcription	Pancreas	Pancrea
47	chr7:116424200-116426800	Weak transcription	Psoas Muscle	Psoas
48	chr7:116424200-116432600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr7:116424200-116440600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr7:116424200-116445400	Weak transcription	Left Ventricle	heart

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