Variant report

Variant	rs6791889
Chromosome Location	chr3:99640716-99640717
allele	A/C
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	chr3:99611356..99613226-chr3:99640035..99641945,2	K562	blood:
2	chr3:99595540..99598482-chr3:99638199..99641058,2	MCF-7	breast:
3	chr3:99592487..99595071-chr3:99639782..99642342,2	MCF-7	breast:
4	chr3:99639074..99641020-chr3:99643167..99645539,2	K562	blood:
5	chr3:99639208..99643794-chr3:99646040..99649673,4	MCF-7	breast:
6	chr3:99638906..99644679-chr3:99646570..99651799,7	K562	blood:
7	chr3:99589828..99592269-chr3:99639312..99642221,3	K562	blood:
8	chr3:99639154..99641723-chr3:99643232..99645940,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs13063594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13073356	1.00[JPT][hapmap]
rs13076199	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[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];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13084413	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13089461	0.87[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];0.85[EUR][1000 genomes]
rs13096116	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]
rs13097830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[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];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34174004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34571898	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35098023	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36077012	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3796131	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62283538	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788894	0.80[AMR][1000 genomes];0.82[EUR][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];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[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];0.92[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:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99604600-99648200	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99619600-99644400	Weak transcription	Right Ventricle	heart
3	chr3:99630600-99644600	Weak transcription	NH-A	brain
4	chr3:99634400-99647400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr3:99637200-99641800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:99637600-99641000	Enhancers	Adipose Nuclei	Adipose
7	chr3:99637600-99641600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:99638200-99641000	Enhancers	Stomach Mucosa	stomach
9	chr3:99638200-99641800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:99638400-99640800	Enhancers	NHEK	skin
11	chr3:99638400-99641000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr3:99638400-99641200	Enhancers	HMEC	breast
13	chr3:99638400-99641400	Enhancers	Fetal Intestine Large	intestine
14	chr3:99638600-99641000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:99638600-99641000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:99638600-99641000	Enhancers	Psoas Muscle	Psoas
17	chr3:99638600-99641000	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr3:99638600-99641200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:99638800-99644200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:99639200-99641000	Enhancers	Brain Cingulate Gyrus	brain
21	chr3:99639200-99641000	Enhancers	Brain Substantia Nigra	brain
22	chr3:99639200-99641000	Enhancers	Ovary	ovary
23	chr3:99639200-99641400	Enhancers	Osteobl	bone
24	chr3:99639400-99641000	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr3:99639400-99641000	Enhancers	Aorta	Aorta
26	chr3:99639400-99641000	Enhancers	Brain Angular Gyrus	brain
27	chr3:99639400-99642200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:99639400-99644000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:99639400-99644000	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:99639600-99641000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:99640000-99641000	Enhancers	HUVEC	blood vessel
32	chr3:99640000-99641400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:99640000-99644000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:99640000-99644000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:99640000-99644600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:99640000-99648400	Weak transcription	HSMMtube	muscle
37	chr3:99640200-99641000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:99640200-99641000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
39	chr3:99640200-99643800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:99640200-99644200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr3:99640200-99644200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:99640200-99644200	Weak transcription	NHDF-Ad	bronchial
43	chr3:99640200-99644400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr3:99640200-99644400	Weak transcription	Brain Anterior Caudate	brain
45	chr3:99640200-99644400	Weak transcription	Hela-S3	cervix
46	chr3:99640200-99648400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:99640200-99648400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:99640400-99640800	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:99640400-99640800	Enhancers	Duodenum Mucosa	Duodenum
50	chr3:99640400-99640800	Weak transcription	NHLF	lung

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