Variant report

Variant	rs1272585
Chromosome Location	chr2:32101059-32101060
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:32093709..32096203-chr2:32099619..32101858,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10439444	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs10490360	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs11124274	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs12475443	0.84[EUR][1000 genomes]
rs12989936	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap]
rs13000753	0.81[ASN][1000 genomes]
rs13017189	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs13024004	0.81[ASN][1000 genomes]
rs160797	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs160801	0.94[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs160803	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17767988	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs1904489	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs223621	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs223665	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs2280967	0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2365555	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2366297	0.80[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41280625	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55730514	0.86[ASN][1000 genomes]
rs62142079	0.82[ASN][1000 genomes]
rs62142080	0.86[ASN][1000 genomes]
rs67157050	0.81[ASN][1000 genomes]
rs6737500	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs6748621	0.85[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.80[LWK][hapmap];0.82[ASN][1000 genomes]
rs6752375	0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs6758024	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs678251	0.80[ASN][1000 genomes]
rs72862234	0.81[ASN][1000 genomes]
rs7370704	0.81[ASN][1000 genomes]
rs7575139	0.81[ASN][1000 genomes]
rs7577696	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7586448	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs7601267	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7608127	0.81[ASN][1000 genomes]
rs7608229	0.81[ASN][1000 genomes]
rs9752651	0.80[EUR][1000 genomes];0.82[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	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv873777	chr2:32019747-32197123	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	esv1801791	chr2:32077901-32120807	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1272585	NLRC4	cis	lymphoblastoid	seeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32057200-32117200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr2:32061600-32172800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:32064600-32142400	Weak transcription	NHDF-Ad	bronchial
4	chr2:32065400-32123000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:32066800-32101800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:32066800-32103400	Weak transcription	Fetal Thymus	thymus
7	chr2:32067000-32106200	Weak transcription	Left Ventricle	heart
8	chr2:32067200-32106000	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:32067800-32103400	Weak transcription	HMEC	breast
10	chr2:32068000-32121400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:32068400-32106800	Weak transcription	Ovary	ovary
12	chr2:32068400-32115400	Weak transcription	NHEK	skin
13	chr2:32068400-32121400	Weak transcription	Fetal Brain Female	brain
14	chr2:32068600-32101800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr2:32068800-32106800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:32069000-32116600	Weak transcription	Osteobl	bone
17	chr2:32071000-32115400	Weak transcription	Placenta	Placenta
18	chr2:32071400-32106000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:32071600-32106000	Weak transcription	Fetal Stomach	stomach
20	chr2:32071800-32116000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr2:32072600-32101800	Weak transcription	Fetal Intestine Small	intestine
22	chr2:32072600-32111800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:32073200-32102000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:32073600-32103000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:32074600-32127000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:32075800-32170000	Weak transcription	Aorta	Aorta
27	chr2:32077200-32115000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:32077200-32116400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:32078200-32101800	Weak transcription	HSMMtube	muscle
30	chr2:32078400-32101800	Weak transcription	Fetal Intestine Large	intestine
31	chr2:32079800-32106400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:32080000-32102200	Weak transcription	Primary B cells from cord blood	blood
33	chr2:32080400-32106000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:32080800-32102000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:32083000-32110600	Weak transcription	Fetal Lung	lung
36	chr2:32083000-32115200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:32085200-32106200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:32086000-32109000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:32086200-32127000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:32086600-32174400	Weak transcription	NHLF	lung
41	chr2:32087400-32103000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:32087600-32115200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr2:32088000-32106400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:32088000-32110800	Weak transcription	Fetal Brain Male	brain
45	chr2:32088000-32116000	Weak transcription	Adipose Nuclei	Adipose
46	chr2:32088000-32157600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:32088200-32127600	Weak transcription	K562	blood
48	chr2:32089400-32160000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:32090000-32103400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:32090000-32116600	Weak transcription	NH-A	brain

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