Variant report

Variant	rs38859
Chromosome Location	chr7:116379094-116379095
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
1	chr7:116366372..116369046-chr7:116379094..116381219,3	MCF-7	breast:
2	chr7:116377829..116379958-chr7:116381598..116383954,2	MCF-7	breast:
3	chr7:116367638..116371989-chr7:116374128..116379673,5	K562	blood:
4	chr7:116374893..116376697-chr7:116378705..116380851,2	K562	blood:
5	chr7:116368864..116371989-chr7:116376223..116379673,4	K562	blood:
6	chr7:116370658..116372962-chr7:116376883..116379609,4	MCF-7	breast:
7	chr7:116363196..116365443-chr7:116378264..116380063,2	MCF-7	breast:
8	chr7:116378415..116380410-chr7:116408724..116411435,2	MCF-7	breast:

No data

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]
rs10435378	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]
rs1049618	1.00[YRI][hapmap]
rs168686	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16945	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs183642	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs187437	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs193688	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]
rs2023748	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2237717	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2299439	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]
rs2402118	0.94[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs35759345	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs38848	0.83[CHB][hapmap]
rs38851	0.82[CHB][hapmap]
rs38854	0.87[CHB][hapmap];0.87[JPT][hapmap];0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs39748	0.83[CHB][hapmap]
rs41735	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41736	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41737	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41738	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41739	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41743	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41744	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41746	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41747	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41748	0.88[EUR][1000 genomes]
rs41749	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41774	1.00[YRI][hapmap]
rs41775	1.00[YRI][hapmap]
rs42229	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs42336	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs42374	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4730762	1.00[YRI][hapmap]
rs6566	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6947629	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6951311	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6978135	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[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	nsv1024485	chr7:116375336-116391582	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs38859	KCND2	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116351800-116407000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr7:116357400-116409800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:116366600-116380800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:116367000-116380800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:116367800-116381200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:116368000-116381200	Weak transcription	Placenta	Placenta
7	chr7:116368200-116380800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:116371400-116380200	Weak transcription	Hela-S3	cervix
9	chr7:116371600-116379200	Genic enhancers	A549	lung
10	chr7:116371800-116382800	Weak transcription	Left Ventricle	heart
11	chr7:116375000-116418400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr7:116375400-116380800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:116375400-116381200	Weak transcription	Pancreas	Pancrea
14	chr7:116375600-116379400	Weak transcription	Fetal Stomach	stomach
15	chr7:116375600-116381400	Weak transcription	Brain Substantia Nigra	brain
16	chr7:116375800-116380000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:116375800-116411200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr7:116376000-116380800	Weak transcription	Gastric	stomach
19	chr7:116376200-116381000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr7:116376600-116379200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr7:116376600-116379200	Enhancers	H9 Cell Line	embryonic stem cell
22	chr7:116376600-116379200	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr7:116376600-116379200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr7:116376600-116379200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr7:116376600-116379200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr7:116376600-116380000	Enhancers	HepG2	liver
27	chr7:116377000-116379800	Weak transcription	NHEK	skin
28	chr7:116377200-116379600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:116377400-116380000	Weak transcription	HSMM	muscle
30	chr7:116377400-116381400	Enhancers	Liver	Liver
31	chr7:116377400-116382800	Weak transcription	Psoas Muscle	Psoas
32	chr7:116377600-116379200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr7:116377600-116379400	Weak transcription	Fetal Muscle Leg	muscle
34	chr7:116377600-116380000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr7:116377600-116380600	Weak transcription	HSMMtube	muscle
36	chr7:116377600-116381400	Weak transcription	Aorta	Aorta
37	chr7:116377800-116379200	Enhancers	Fetal Lung	lung
38	chr7:116377800-116380000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr7:116377800-116380800	Weak transcription	Fetal Intestine Small	intestine
40	chr7:116377800-116380800	Weak transcription	HMEC	breast
41	chr7:116377800-116395600	Weak transcription	NH-A	brain
42	chr7:116378000-116379600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr7:116378000-116381200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr7:116378000-116381600	Weak transcription	Fetal Intestine Large	intestine
45	chr7:116378000-116389000	Weak transcription	Stomach Mucosa	stomach
46	chr7:116378200-116380400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr7:116378200-116381000	Enhancers	HUVEC	blood vessel
48	chr7:116378400-116379200	Enhancers	Fetal Kidney	kidney
49	chr7:116378600-116379800	Weak transcription	Osteobl	bone
50	chr7:116378600-116381400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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