Variant report

Variant	rs2999552
Chromosome Location	chr1:152008766-152008767
allele	A/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:30)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:152008579..152009679-chr9:96928359..96929023,3	Hela-S3	cervix:
2	chr1:152004043..152013121-chr1:152013584..152022966,19	K562	blood:
3	chr1:152007819..152009506-chr20:60812730..60815598,2	MCF-7	breast:
4	chr1:152008726..152009579-chr16:30087254..30087774,2	Hela-S3	cervix:
5	chr1:152008633..152009375-chr8:128231144..128232068,2	Hela-S3	cervix:
6	chr1:151880418..151883577-chr1:152005621..152009474,7	MCF-7	breast:
7	chr1:152006929..152009438-chr1:152146251..152148061,2	MCF-7	breast:
8	chr1:151958520..151979218-chr1:151992734..152014750,97	MCF-7	breast:
9	chr1:150551625..150552492-chr1:152008328..152009203,2	Hela-S3	cervix:
10	chr1:152008730..152009529-chr8:145159142..145160024,2	Hela-S3	cervix:
11	chr1:152008581..152009552-chr1:244997727..244998825,3	Hela-S3	cervix:
12	chr1:152008668..152009656-chr12:50135014..50135816,3	Hela-S3	cervix:
13	chr1:152008592..152010631-chr1:153605290..153607916,2	MCF-7	breast:
14	chr1:151738370..151740196-chr1:152006086..152008805,2	MCF-7	breast:
15	chr1:152007310..152009058-chr1:152155234..152157493,3	MCF-7	breast:
16	chr1:152007737..152009459-chr1:152068857..152070945,2	MCF-7	breast:
17	chr1:152008149..152008806-chr17:58602920..58603730,2	MCF-7	breast:
18	chr1:152007122..152009861-chr1:152059788..152062701,3	MCF-7	breast:
19	chr1:151949201..151951606-chr1:152006321..152008860,3	MCF-7	breast:
20	chr1:151879656..151883388-chr1:152007614..152010954,7	K562	blood:
21	chr1:151856848..151858901-chr1:152006304..152009050,2	K562	blood:
22	chr1:152007812..152009419-chr11:65774056..65776325,2	MCF-7	breast:
23	chr1:152008052..152008847-chr1:152020250..152020815,2	Hela-S3	cervix:
24	chr1:151905962..151909275-chr1:152006477..152009403,3	K562	blood:
25	chr1:151879353..151883785-chr1:152005989..152009719,8	K562	blood:
26	chr1:151804439..151806613-chr1:152006311..152009166,3	MCF-7	breast:
27	chr1:152004094..152009269-chr1:152022985..152027910,7	K562	blood:
28	chr1:151862292..151864309-chr1:152006285..152009037,3	MCF-7	breast:
29	chr1:151812161..151813920-chr1:152008098..152012154,3	MCF-7	breast:
30	chr1:152007001..152009228-chr1:152088352..152090668,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272030	Chromatin interaction
ENSG00000225556	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000247844	Chromatin interaction
ENSG00000179632	Chromatin interaction
ENSG00000182898	Chromatin interaction
ENSG00000259349	Chromatin interaction
ENSG00000130703	Chromatin interaction
ENSG00000159445	Chromatin interaction
ENSG00000062725	Chromatin interaction
ENSG00000197747	Chromatin interaction
ENSG00000229021	Chromatin interaction
ENSG00000268288	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000149923	Chromatin interaction
ENSG00000269946	Chromatin interaction
ENSG00000143450	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000203667	Chromatin interaction
ENSG00000179526	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

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];1.00[CHB][hapmap]
rs11578030	1.00[CHB][hapmap]
rs12723616	1.00[CHB][hapmap]
rs1387834	1.00[CHB][hapmap]
rs1387835	1.00[CHB][hapmap]
rs1490187	1.00[CHB][hapmap]
rs1490191	1.00[CHB][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]
rs1873310	1.00[CHB][hapmap]
rs1873311	1.00[CHB][hapmap]
rs1873312	1.00[CHB][hapmap]
rs1967085	1.00[CHB][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]
rs2999535	1.00[CHB][hapmap]
rs2999536	1.00[CHB][hapmap]
rs2999537	1.00[CHB][hapmap]
rs2999538	1.00[CHB][hapmap]
rs2999547	1.00[JPT][hapmap]
rs2999550	0.90[ASN][1000 genomes]
rs2999551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999553	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999554	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2999555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2999558	1.00[CHB][hapmap]
rs2999559	0.91[ASN][1000 genomes]
rs3001979	1.00[CHB][hapmap]
rs3007671	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3007672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3007673	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3007674	0.97[ASN][1000 genomes]
rs3007676	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]
rs3007677	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007678	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3007679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3007690	1.00[CHB][hapmap]
rs3007700	1.00[CHB][hapmap]
rs3007701	1.00[CHB][hapmap]
rs3007704	1.00[CHB][hapmap]
rs3122300	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3122302	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3122303	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3122304	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3134814	1.00[CHB][hapmap]
rs3811422	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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]
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]
rs9943225	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv547853	chr1:152008671-152236760	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2999552	LOC729659///LOC730278	trans	lymphoblastoid	RTeQTL
rs2999552	S100A11	Cis_1M	lymphoblastoid	RTeQTL
rs2999552	S100A11	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152006400-152010000	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr1:152006600-152009600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:152006600-152010000	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr1:152006800-152008800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:152006800-152009200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr1:152006800-152009800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr1:152006800-152009800	Active TSS	Right Ventricle	heart
8	chr1:152006800-152010000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr1:152006800-152010000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:152006800-152010000	Active TSS	Esophagus	oesophagus
11	chr1:152007000-152009600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:152007000-152009800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:152007000-152009800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:152007000-152009800	Active TSS	Placenta Amnion	Placenta Amnion
15	chr1:152007000-152009800	Active TSS	HSMM	muscle
16	chr1:152007000-152010000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:152007200-152008800	Flanking Active TSS	Primary B cells from peripheral blood	blood
18	chr1:152007200-152009400	Active TSS	Brain Anterior Caudate	brain
19	chr1:152007200-152009600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:152007200-152009600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:152007200-152009600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:152007200-152009600	Active TSS	Lung	lung
23	chr1:152007200-152009800	Active TSS	Aorta	Aorta
24	chr1:152007200-152009800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
25	chr1:152007200-152010200	Active TSS	Gastric	stomach
26	chr1:152007400-152009400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr1:152007400-152009400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:152007400-152009800	Active TSS	NHLF	lung
29	chr1:152007400-152010000	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr1:152007600-152009600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:152007600-152009600	Active TSS	Left Ventricle	heart
32	chr1:152007600-152009600	Active TSS	Thymus	Thymus
33	chr1:152007600-152009800	Active TSS	H9 Cell Line	embryonic stem cell
34	chr1:152007600-152009800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:152007600-152009800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:152007600-152009800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:152007600-152009800	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr1:152007600-152009800	Active TSS	Right Atrium	heart
39	chr1:152007800-152009400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:152007800-152009600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:152007800-152009600	Active TSS	Fetal Intestine Large	intestine
42	chr1:152007800-152009600	Active TSS	Fetal Intestine Small	intestine
43	chr1:152007800-152009600	Active TSS	Placenta	Placenta
44	chr1:152007800-152009600	Active TSS	Stomach Mucosa	stomach
45	chr1:152007800-152009600	Active TSS	Hela-S3	cervix
46	chr1:152007800-152009800	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr1:152007800-152009800	Active TSS	Psoas Muscle	Psoas
48	chr1:152007800-152009800	Active TSS	Rectal Smooth Muscle	rectum
49	chr1:152007800-152009800	Active TSS	NHDF-Ad	bronchial
50	chr1:152007800-152010000	Active TSS	HSMMtube	muscle

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