Variant report

Variant	rs3007672
Chromosome Location	chr1:152000478-152000479
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	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	chr1:151879382..151882354-chr1:151997531..152001946,4	MCF-7	breast:
7	chr1:151942667..151945612-chr1:151998749..152001571,2	MCF-7	breast:
8	chr1:151943551..151945492-chr1:151999086..152000598,2	K562	blood:

No data

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

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1003107	1.00[CHB][hapmap]
rs10158030	1.00[CHB][hapmap]
rs1038746	1.00[CHB][hapmap]
rs1038748	1.00[CHB][hapmap]
rs10788813	1.00[CHB][hapmap]
rs10788816	1.00[CHB][hapmap]
rs10888453	1.00[CHB][hapmap]
rs11204911	1.00[CHB][hapmap]
rs11204912	1.00[CHB][hapmap]
rs11204923	0.82[CEU][hapmap]
rs11578030	1.00[CHB][hapmap]
rs12723616	1.00[CHB][hapmap]
rs1387834	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs1387835	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs1490187	1.00[CHB][hapmap]
rs1490191	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs1496037	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[ASN][1000 genomes]
rs1552606	1.00[CHB][hapmap]
rs1552607	1.00[CHB][hapmap]
rs1602245	1.00[CHB][hapmap]
rs1602248	1.00[CHB][hapmap]
rs17583707	1.00[CHB][hapmap]
rs1873311	1.00[CHB][hapmap]
rs1873312	1.00[CHB][hapmap]
rs1967085	1.00[CHB][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs2338018	1.00[CHB][hapmap]
rs2932563	1.00[CHB][hapmap]
rs2932567	1.00[CHB][hapmap]
rs2932592	1.00[CHB][hapmap]
rs2999514	1.00[CHB][hapmap]
rs2999527	1.00[CHB][hapmap]
rs2999529	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs2999535	1.00[CHB][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs2999536	1.00[CHB][hapmap]
rs2999537	1.00[CHB][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs2999538	1.00[CHB][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs2999547	0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2999551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999553	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999554	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[EUR][1000 genomes]
rs2999558	1.00[CHB][hapmap]
rs2999562	1.00[ASN][1000 genomes]
rs3001979	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3007671	1.00[JPT][hapmap]
rs3007673	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3007677	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3007678	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs3007690	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3007700	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3007701	1.00[CHB][hapmap]
rs3007704	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3104205	0.81[ASN][1000 genomes]
rs3122300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3122301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3122302	0.90[EUR][1000 genomes]
rs3122303	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122304	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3134814	1.00[CHB][hapmap];0.83[AFR][1000 genomes]
rs3811422	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845385	1.00[CHB][hapmap]
rs4845388	1.00[CHB][hapmap]
rs4845393	1.00[CHB][hapmap]
rs4845660	1.00[CHB][hapmap]
rs4845664	1.00[CHB][hapmap]
rs6587626	1.00[CHB][hapmap]
rs6587628	1.00[CHB][hapmap]
rs6587629	1.00[CHB][hapmap]
rs6587630	1.00[CHB][hapmap]
rs6587641	1.00[CHB][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs6659029	1.00[CHB][hapmap]
rs6685291	1.00[CHB][hapmap]
rs6691350	1.00[CHB][hapmap]
rs7529451	1.00[CHB][hapmap]
rs7532721	1.00[CHB][hapmap]
rs902314	1.00[CHB][hapmap]
rs902315	1.00[CHB][hapmap]
rs959945	1.00[CHB][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs9943225	1.00[CHB][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3007672	S100A11	cis	lymphoblastoid	seeQTL
rs3007672	LOC729659///LOC730278	trans	lymphoblastoid	RTeQTL
rs3007672	S100A11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 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	chr1:151996800-152004000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:151997000-152001200	Weak transcription	Placenta	Placenta
11	chr1:151997000-152003400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:151997000-152004200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:151997000-152004400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:151997000-152004800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:151997000-152006600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:151997000-152007000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:151997200-152001600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:151997600-152001400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:151997800-152001400	Weak transcription	Esophagus	oesophagus
20	chr1:151997800-152003200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:151997800-152003400	Weak transcription	Lung	lung
22	chr1:151998600-152003000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:151998800-152000600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:151998800-152002800	Enhancers	HMEC	breast
25	chr1:151999000-152004200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:151999200-152002600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr1:151999200-152002600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:151999400-152004000	Weak transcription	Aorta	Aorta
29	chr1:151999600-152001600	Weak transcription	Primary T cells from cord blood	blood
30	chr1:151999600-152003400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:151999600-152003400	Weak transcription	NH-A	brain
32	chr1:151999800-152001600	Weak transcription	A549	lung
33	chr1:151999800-152002600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:152000000-152004000	Weak transcription	NHLF	lung
35	chr1:152000200-152001200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:152000200-152001200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:152000200-152001400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:152000200-152001600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:152000200-152001600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:152000200-152005000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:152000400-152001400	Weak transcription	NHEK	skin
42	chr1:152000400-152004200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:152000400-152004600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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