Variant report

Variant	rs3007671
Chromosome Location	chr1:151999347-151999348
allele	G/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151999004..152000652-chr1:152126763..152128781,2	MCF-7	breast:
2	chr1:151958520..151979218-chr1:151992734..152014750,97	MCF-7	breast:
3	chr1:151880174..151882015-chr1:151999155..152001089,2	MCF-7	breast:
4	chr1:151910939..151913663-chr1:151998733..152000964,2	MCF-7	breast:
5	chr1:151998303..152000885-chr14:71732498..71734961,2	MCF-7	breast:
6	chr1:151997592..152000078-chr1:152004564..152007278,3	K562	blood:
7	chr1:151879382..151882354-chr1:151997531..152001946,4	MCF-7	breast:
8	chr1:151942667..151945612-chr1:151998749..152001571,2	MCF-7	breast:
9	chr1:151943551..151945492-chr1:151999086..152000598,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000229021	Chromatin interaction
ENSG00000197747	Chromatin interaction
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11578030	1.00[CHB][hapmap]
rs12123975	0.87[TSI][hapmap]
rs12134184	0.87[TSI][hapmap]
rs2999536	1.00[CHB][hapmap]
rs2999547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2999550	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2999551	1.00[JPT][hapmap]
rs2999552	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2999555	1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2999559	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3007672	1.00[JPT][hapmap]
rs3007674	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007676	1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3007677	0.97[ASN][1000 genomes]
rs3007679	1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3007704	1.00[CHB][hapmap]
rs3122300	1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3122301	1.00[JPT][hapmap]
rs3122302	0.88[ASN][1000 genomes]
rs3811422	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3007671	KCNK5	trans	cerebellum	SCAN
rs3007671	S100A8	cis	parietal	SCAN
rs3007671	LASS2	cis	parietal	SCAN
rs3007671	PSMB4	cis	cerebellum	SCAN
rs3007671	SELENBP1	cis	cerebellum	SCAN
rs3007671	S100A10	cis	cerebellum	SCAN
rs3007671	LCE2C	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151986800-152007400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:151988600-152002600	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:151988600-152004000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:151993400-152003000	Weak transcription	Fetal Intestine Small	intestine
5	chr1:151994000-152002400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:151994400-152003200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:151995600-152001200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:151996600-152004400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:151996800-152000200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:151996800-152004000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:151997000-152001200	Weak transcription	Placenta	Placenta
12	chr1:151997000-152003400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:151997000-152004200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:151997000-152004400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:151997000-152004800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:151997000-152006600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:151997000-152007000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:151997200-152001600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:151997600-152001400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:151997800-152001400	Weak transcription	Esophagus	oesophagus
21	chr1:151997800-152003200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:151997800-152003400	Weak transcription	Lung	lung
23	chr1:151998600-152003000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:151998800-152000600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:151998800-152002800	Enhancers	HMEC	breast
26	chr1:151999000-152004200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:151999200-151999400	Enhancers	Aorta	Aorta
28	chr1:151999200-151999400	Bivalent Enhancer	NH-A	brain
29	chr1:151999200-152000200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:151999200-152000400	Enhancers	NHEK	skin
31	chr1:151999200-152002600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr1:151999200-152002600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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