Variant report

Variant	rs13096116
Chromosome Location	chr3:99632259-99632260
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99624361..99628142-chr3:99629982..99633873,3	MCF-7	breast:
2	chr3:99595655..99597769-chr3:99630372..99633111,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13060898	1.00[JPT][hapmap]
rs13063594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13073356	1.00[JPT][hapmap]
rs13076199	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13081855	0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs13082013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13084413	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13089461	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13095282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13097830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13100490	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17778253	1.00[JPT][hapmap];0.85[MEX][hapmap]
rs34174004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34571898	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35098023	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36077012	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62283538	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788894	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6791889	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626245	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7636514	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs7647466	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs7649862	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes]

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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99600800-99638600	Weak transcription	Left Ventricle	heart
2	chr3:99604600-99648200	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99619600-99644400	Weak transcription	Right Ventricle	heart
4	chr3:99620000-99638600	Weak transcription	Small Intestine	intestine
5	chr3:99621200-99638600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:99625000-99632800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:99625000-99639400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:99627200-99638600	Weak transcription	K562	blood
9	chr3:99629000-99639400	Weak transcription	HSMM	muscle
10	chr3:99630000-99634400	Weak transcription	HepG2	liver
11	chr3:99630000-99637600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:99630000-99638200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:99630400-99638400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:99630600-99633200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:99630600-99638000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:99630600-99638000	Weak transcription	Osteobl	bone
17	chr3:99630600-99638600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:99630600-99638600	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:99630600-99638600	Weak transcription	Pancreas	Pancrea
20	chr3:99630600-99638800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr3:99630600-99644600	Weak transcription	NH-A	brain
22	chr3:99630800-99633000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:99630800-99638400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:99631200-99633000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:99631200-99634600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:99631200-99638400	Weak transcription	NHEK	skin
27	chr3:99631400-99638400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:99631400-99638600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:99631800-99639800	Weak transcription	Primary B cells from cord blood	blood
30	chr3:99632200-99635000	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links