Variant report

Variant	rs3007676
Chromosome Location	chr1:152007599-152007600
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:32)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:152004043..152013121-chr1:152013584..152022966,19	K562	blood:
2	chr1:152006746..152007691-chr1:152024759..152025648,5	MCF-7	breast:
3	chr1:152006256..152008439-chr1:152160250..152162378,2	MCF-7	breast:
4	chr1:151880418..151883577-chr1:152005621..152009474,7	MCF-7	breast:
5	chr1:152007275..152008195-chr9:100954315..100955028,2	Hela-S3	cervix:
6	chr1:152006929..152009438-chr1:152146251..152148061,2	MCF-7	breast:
7	chr1:151958520..151979218-chr1:151992734..152014750,97	MCF-7	breast:
8	chr1:151972354..151974327-chr1:152005539..152008524,2	K562	blood:
9	chr1:152004872..152007775-chr21:40685504..40687416,2	MCF-7	breast:
10	chr1:151738370..151740196-chr1:152006086..152008805,2	MCF-7	breast:
11	chr1:152007037..152007811-chr19:49990585..49991385,2	Hela-S3	cervix:
12	chr1:152007310..152009058-chr1:152155234..152157493,3	MCF-7	breast:
13	chr1:152006888..152007857-chr10:38265085..38265598,2	Hela-S3	cervix:
14	chr1:152007159..152007857-chr10:103124610..103125126,2	Hela-S3	cervix:
15	chr1:152007411..152008346-chr1:152020191..152020876,2	MCF-7	breast:
16	chr1:152007122..152009861-chr1:152059788..152062701,3	MCF-7	breast:
17	chr1:151949201..151951606-chr1:152006321..152008860,3	MCF-7	breast:
18	chr1:152007524..152008240-chr1:152020437..152021287,2	MCF-7	breast:
19	chr1:152007427..152008232-chr8:71580861..71581794,2	Hela-S3	cervix:
20	chr1:151856848..151858901-chr1:152006304..152009050,2	K562	blood:
21	chr1:151905962..151909275-chr1:152006477..152009403,3	K562	blood:
22	chr1:151879353..151883785-chr1:152005989..152009719,8	K562	blood:
23	chr1:151965160..151967590-chr1:152005714..152007860,2	K562	blood:
24	chr1:152004874..152008437-chr1:152153479..152155850,3	MCF-7	breast:
25	chr1:152006962..152007668-chr7:10979482..10980090,2	Hela-S3	cervix:
26	chr1:152006733..152007820-chr1:152020148..152021009,8	MCF-7	breast:
27	chr1:151804439..151806613-chr1:152006311..152009166,3	MCF-7	breast:
28	chr1:151400521..151402595-chr1:152006096..152008754,2	MCF-7	breast:
29	chr1:152004094..152009269-chr1:152022985..152027910,7	K562	blood:
30	chr1:151862292..151864309-chr1:152006285..152009037,3	MCF-7	breast:
31	chr1:152007316..152008232-chr2:28612874..28613437,2	Hela-S3	cervix:
32	chr1:152007001..152009228-chr1:152088352..152090668,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143442	Chromatin interaction
ENSG00000142541	Chromatin interaction
ENSG00000106789	Chromatin interaction
ENSG00000182898	Chromatin interaction
ENSG00000237975	Chromatin interaction
ENSG00000143450	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000175395	Chromatin interaction
ENSG00000268288	Chromatin interaction
ENSG00000271185	Chromatin interaction
ENSG00000189043	Chromatin interaction
ENSG00000197747	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000221947	Chromatin interaction
ENSG00000222414	Chromatin interaction
ENSG00000147592	Chromatin interaction
ENSG00000229021	Chromatin interaction
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

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]
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	1.00[JPT][hapmap]
rs2999550	0.90[ASN][1000 genomes]
rs2999551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2999552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999553	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2999554	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2999555	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[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2999558	1.00[CHB][hapmap]
rs2999559	0.91[ASN][1000 genomes]
rs3001979	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3007671	1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3007672	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]
rs3007673	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3007674	0.97[ASN][1000 genomes]
rs3007677	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007678	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3007679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[ASN][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]
rs3122300	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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3122302	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3122303	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3122304	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3134814	1.00[CHB][hapmap]
rs3811422	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][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
rs3007676	S100A11	Cis_1M	lymphoblastoid	RTeQTL
rs3007676	S100A11	cis	lymphoblastoid	seeQTL
rs3007676	LOC729659///LOC730278	trans	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152005200-152008200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
2	chr1:152005400-152008400	Transcr. at gene 5' and 3'	NHEK	skin
3	chr1:152005600-152007600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:152005600-152008600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:152005800-152008400	Weak transcription	Ovary	ovary
6	chr1:152006000-152008200	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
7	chr1:152006000-152008200	Transcr. at gene 5' and 3'	HMEC	breast
8	chr1:152006200-152008400	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr1:152006400-152008000	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:152006400-152008000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
11	chr1:152006400-152008200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr1:152006400-152010000	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr1:152006600-152007600	Flanking Active TSS	Thymus	Thymus
14	chr1:152006600-152007800	Flanking Active TSS	Placenta	Placenta
15	chr1:152006600-152008000	Flanking Active TSS	K562	blood
16	chr1:152006600-152008200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr1:152006600-152008200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr1:152006600-152008200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr1:152006600-152008400	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr1:152006600-152008600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr1:152006600-152009600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:152006600-152010000	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr1:152006800-152007600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:152006800-152007600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:152006800-152007600	Flanking Active TSS	Left Ventricle	heart
26	chr1:152006800-152007800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:152006800-152007800	Flanking Active TSS	Fetal Intestine Large	intestine
28	chr1:152006800-152007800	Flanking Active TSS	Fetal Intestine Small	intestine
29	chr1:152006800-152007800	Flanking Active TSS	HSMMtube	muscle
30	chr1:152006800-152008000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr1:152006800-152008000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:152006800-152008200	Flanking Active TSS	Fetal Lung	lung
33	chr1:152006800-152008200	Flanking Active TSS	Fetal Thymus	thymus
34	chr1:152006800-152008200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr1:152006800-152008200	Flanking Active TSS	HUVEC	blood vessel
36	chr1:152006800-152008400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr1:152006800-152008400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:152006800-152008600	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr1:152006800-152008800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:152006800-152009200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr1:152006800-152009800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr1:152006800-152009800	Active TSS	Right Ventricle	heart
43	chr1:152006800-152010000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr1:152006800-152010000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:152006800-152010000	Active TSS	Esophagus	oesophagus
46	chr1:152007000-152007600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:152007000-152007600	Active TSS	A549	lung
48	chr1:152007000-152007800	Active TSS	Stomach Smooth Muscle	stomach
49	chr1:152007000-152007800	Flanking Active TSS	Hela-S3	cervix
50	chr1:152007000-152008000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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