Variant report

Variant	rs1009954
Chromosome Location	chr12:11898099-11898100
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:11898044..11900698-chr12:11957221..11959288,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1009951	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1009953	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10743967	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10845408	0.88[CEU][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs11054421	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11054423	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11054424	0.86[EUR][1000 genomes]
rs11054429	0.87[EUR][1000 genomes]
rs11054433	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11054439	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs11615175	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs12369491	0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs17818461	0.81[CEU][hapmap];0.91[CHB][hapmap];0.80[EUR][1000 genomes]
rs17818498	0.88[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs17818624	0.92[CEU][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs2051525	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2187642	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2724588	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2724599	0.82[EUR][1000 genomes]
rs2724600	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2724616	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2724618	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2724633	0.92[CEU][hapmap];0.84[JPT][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2724635	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.99[ASN][1000 genomes]
rs2724645	0.82[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2724648	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2856321	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2856322	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2856324	0.82[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2856338	0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs2856344	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2900208	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs2954980	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4763719	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs762717	0.82[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
2	nsv1053609	chr12:11898099-11933906	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1009954	NECAP1	cis	cerebellum	SCAN
rs1009954	KLRA1	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11873200-11902400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:11873200-11909400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:11882400-11899200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:11882400-11902600	Weak transcription	Fetal Muscle Leg	muscle
5	chr12:11882400-11903200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:11883800-11906000	Weak transcription	Liver	Liver
7	chr12:11884200-11899000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:11885200-11906200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:11885600-11898600	Weak transcription	Primary T cells from cord blood	blood
10	chr12:11885600-11899000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:11885600-11905200	Weak transcription	Fetal Intestine Large	intestine
12	chr12:11885800-11898400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:11885800-11911600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr12:11886000-11900000	Weak transcription	Colonic Mucosa	Colon
15	chr12:11889800-11901800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr12:11890000-11902400	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:11892400-11898600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:11893200-11915000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr12:11893800-11901200	Enhancers	HMEC	breast
20	chr12:11894400-11898800	Weak transcription	Right Atrium	heart
21	chr12:11894400-11899000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr12:11894600-11898200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:11894600-11898200	Weak transcription	Gastric	stomach
24	chr12:11894600-11898400	Weak transcription	Pancreas	Pancrea
25	chr12:11894600-11898400	Weak transcription	NH-A	brain
26	chr12:11894600-11898600	Weak transcription	Osteobl	bone
27	chr12:11894600-11898800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:11894600-11905200	Weak transcription	Fetal Intestine Small	intestine
29	chr12:11894600-11905400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:11894600-11905400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr12:11894600-11906200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:11894600-11908400	Weak transcription	Psoas Muscle	Psoas
33	chr12:11894800-11899200	Weak transcription	HSMM	muscle
34	chr12:11894800-11906000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:11894800-11906600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:11895000-11898200	Weak transcription	Small Intestine	intestine
37	chr12:11895000-11899200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:11895000-11906000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:11895000-11906800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:11895000-11912600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:11895400-11906000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:11895400-11914400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:11895600-11908800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr12:11895800-11901200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:11896000-11906200	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr12:11896200-11899600	Enhancers	Colon Smooth Muscle	Colon
47	chr12:11896200-11900200	Enhancers	Rectal Smooth Muscle	rectum
48	chr12:11896400-11898400	Genic enhancers	Primary B cells from cord blood	blood
49	chr12:11896400-11898400	Genic enhancers	Fetal Thymus	thymus
50	chr12:11896400-11900400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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