Variant report

Variant	rs2959880
Chromosome Location	chr11:63438836-63438837
allele	A/G
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:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:63437372..63440690-chr11:63447067..63450757,11	K562	blood:
2	chr1:249200344..249200946-chr11:63438364..63439120,2	Hela-S3	cervix:
3	chr11:63437085..63438927-chr11:63580871..63582709,2	MCF-7	breast:
4	chr11:63438386..63439207-chr5:43120977..43121927,2	Hela-S3	cervix:
5	chr11:63436138..63441406-chr11:63446930..63451361,18	MCF-7	breast:
6	chr11:63438103..63439872-chr16:87424140..87427090,2	MCF-7	breast:
7	chr11:63429933..63433001-chr11:63436097..63439053,5	K562	blood:
8	chr11:63436203..63440489-chr11:63447864..63452214,13	MCF-7	breast:
9	chr11:63437417..63439651-chr11:63532413..63534182,2	MCF-7	breast:
10	chr11:63437875..63444495-chr11:63445155..63450267,13	K562	blood:
11	chr11:63437085..63438934-chr11:63535581..63537340,2	MCF-7	breast:
12	chr11:63438157..63438845-chr11:63506421..63507029,2	MCF-7	breast:
13	chr11:63437131..63441413-chr11:63464952..63468959,4	MCF-7	breast:
14	chr11:63438290..63439108-chr18:3247373..3247936,2	Hela-S3	cervix:
15	chr1:244998597..244999470-chr11:63438295..63438902,2	Hela-S3	cervix:
16	chr11:63437518..63440264-chr11:63931610..63934606,2	MCF-7	breast:
17	chr11:63437870..63440205-chr11:63606706..63609553,2	MCF-7	breast:
18	chr11:63438402..63439044-chr15:41056120..41056646,2	Hela-S3	cervix:
19	chr11:63436319..63439202-chr11:63579775..63581446,2	MCF-7	breast:
20	chr11:63438291..63439207-chr19:2476045..2476569,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000203667	Chromatin interaction
ENSG00000099860	Chromatin interaction
ENSG00000271100	Chromatin interaction
ENSG00000103264	Chromatin interaction
ENSG00000188070	Chromatin interaction
ENSG00000185220	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000133315	Chromatin interaction
ENSG00000072518	Chromatin interaction
ENSG00000168005	Chromatin interaction
ENSG00000133318	Chromatin interaction
ENSG00000255651	Chromatin interaction
ENSG00000137880	Chromatin interaction
ENSG00000140941	Chromatin interaction
ENSG00000101608	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10501394	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231535	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231543	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231545	1.00[CEU][hapmap]
rs11551942	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11551944	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11820129	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1186941	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211688	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12274980	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17158453	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656941	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1789219	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2509744	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959876	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959881	0.91[EUR][1000 genomes]
rs2959886	0.89[EUR][1000 genomes]
rs3016865	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34109368	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35345497	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35754698	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934131	0.83[CEU][hapmap]
rs4405320	0.83[CEU][hapmap]
rs474548	0.85[MEX][hapmap]
rs476034	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476691	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482915	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484619	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491231	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500726	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs500991	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511819	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515645	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517700	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518490	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518692	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521464	1.00[CEU][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523093	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523809	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534505	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534876	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539306	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541809	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs542998	0.85[MEX][hapmap]
rs550629	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551466	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557882	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559405	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs560938	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562549	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566255	0.85[MEX][hapmap]
rs566813	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567756	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568769	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568790	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580695	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588523	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928162	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928163	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928165	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928166	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928167	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928168	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928195	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928196	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928197	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928202	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928203	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928204	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928205	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928206	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928208	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928209	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928211	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928212	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928214	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928234	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928236	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928237	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928238	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928239	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928241	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928243	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928244	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928245	0.90[EUR][1000 genomes]
rs61928246	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928247	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928248	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61929731	0.88[EUR][1000 genomes]
rs6591821	0.92[EUR][1000 genomes]
rs6591822	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106670	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111395	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7116486	0.83[CEU][hapmap]
rs7117206	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7119961	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127454	1.00[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128040	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128970	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7928900	1.00[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7931908	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7932117	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7939940	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943981	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7944003	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7944094	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945972	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949389	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949447	0.97[EUR][1000 genomes];1.00[ASN][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	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv832183	chr11:63416678-63564565	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2959880	SNORD25	cis	parietal	SCAN
rs2959880	SLC22A9	cis	cerebellum	SCAN
rs2959880	RASGRP2	cis	parietal	SCAN
rs2959880	MTA2	cis	cerebellum	SCAN
rs2959880	PLA2G16	cis	cerebellum	SCAN
rs2959880	FLRT1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63437200-63439200	Active TSS	NHDF-Ad	bronchial
2	chr11:63437200-63439400	Active TSS	NHLF	lung
3	chr11:63437200-63439600	Active TSS	HSMM	muscle
4	chr11:63437400-63439200	Active TSS	Aorta	Aorta
5	chr11:63437400-63439200	Active TSS	Psoas Muscle	Psoas
6	chr11:63437400-63439200	Active TSS	GM12878-XiMat	blood
7	chr11:63437400-63439200	Active TSS	K562	blood
8	chr11:63437400-63439400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:63437400-63439400	Active TSS	A549	lung
10	chr11:63437600-63439000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr11:63437600-63439000	Active TSS	Right Ventricle	heart
12	chr11:63437600-63439200	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:63437600-63439200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:63437600-63439200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr11:63437600-63439200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:63437600-63439200	Active TSS	Muscle Satellite Cultured Cells	--
17	chr11:63437600-63439200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr11:63437600-63439200	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr11:63437600-63439200	Active TSS	Fetal Muscle Trunk	muscle
20	chr11:63437600-63439200	Active TSS	Ovary	ovary
21	chr11:63437600-63439200	Active TSS	Stomach Smooth Muscle	stomach
22	chr11:63437600-63439400	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr11:63437600-63439600	Active TSS	Brain Angular Gyrus	brain
24	chr11:63437600-63439600	Active TSS	Right Atrium	heart
25	chr11:63437800-63439200	Active TSS	H9 Cell Line	embryonic stem cell
26	chr11:63437800-63439200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:63437800-63439200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:63437800-63439200	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr11:63437800-63439200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:63437800-63439200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:63437800-63439200	Active TSS	Colonic Mucosa	Colon
32	chr11:63437800-63439200	Active TSS	Fetal Intestine Large	intestine
33	chr11:63437800-63439200	Active TSS	Fetal Muscle Leg	muscle
34	chr11:63437800-63439200	Active TSS	Fetal Stomach	stomach
35	chr11:63437800-63439200	Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr11:63437800-63439200	Active TSS	NHEK	skin
37	chr11:63437800-63439400	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr11:63437800-63439400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:63437800-63439400	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr11:63437800-63439400	Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr11:63437800-63439400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr11:63437800-63439400	Active TSS	Colon Smooth Muscle	Colon
43	chr11:63437800-63439400	Active TSS	Rectal Smooth Muscle	rectum
44	chr11:63437800-63439600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr11:63437800-63439600	Active TSS	Fetal Intestine Small	intestine
46	chr11:63438000-63439200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:63438000-63439200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr11:63438000-63439200	Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr11:63438000-63439200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr11:63438000-63439200	Active TSS	Primary T killer memory cells from peripheral blood	blood

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