Variant report

Variant	rs11163900
Chromosome Location	chr1:84557569-84557570
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:84541438..84545739-chr1:84555567..84558104,4	K562	blood:
2	chr1:84553847..84557736-chr1:84560723..84565476,4	K562	blood:
3	chr1:84550027..84551748-chr1:84557212..84559116,2	MCF-7	breast:
4	chr1:84556236..84558984-chr1:84559547..84561523,2	MCF-7	breast:
5	chr1:84554743..84559247-chr1:84561300..84565476,7	K562	blood:

Variant related genes	Relation type
ENSG00000213540	Chromatin interaction
ENSG00000271576	Chromatin interaction
ENSG00000142875	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1021490	0.86[AMR][1000 genomes]
rs10493750	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874428	0.81[GIH][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs11163897	0.80[JPT][hapmap]
rs11163898	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11163903	0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs11163905	0.88[GIH][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs11163906	0.88[ASW][hapmap];0.88[GIH][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes]
rs11163907	0.88[GIH][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs11163908	0.80[AMR][1000 genomes]
rs12057561	0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs12064926	0.80[AMR][1000 genomes]
rs12070547	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12094426	0.80[AMR][1000 genomes]
rs12119275	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs12132032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12404263	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[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];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12405120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12565896	0.83[MEX][hapmap]
rs12723299	0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs12724598	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12746741	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12748859	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs12759624	0.80[AMR][1000 genomes]
rs12760594	0.80[AMR][1000 genomes]
rs1402694	0.88[GIH][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs1472243	0.82[AMR][1000 genomes]
rs1521518	0.88[GIH][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs1565823	0.81[GIH][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs1874070	0.84[GIH][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs2037454	0.81[GIH][hapmap]
rs2134646	0.83[MEX][hapmap]
rs2134647	0.83[MEX][hapmap]
rs2134648	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs34179759	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34495740	0.93[ASN][1000 genomes]
rs35452337	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3861699	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs6576960	0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs6576962	0.88[GIH][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs6576963	0.83[MEX][hapmap]
rs6661492	0.80[AMR][1000 genomes]
rs6669045	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674038	0.80[JPT][hapmap]
rs6695305	0.80[AMR][1000 genomes]
rs6696125	0.81[GIH][hapmap];0.83[MEX][hapmap]
rs6703653	0.90[JPT][hapmap]
rs67276144	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72711192	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512288	0.80[AMR][1000 genomes]
rs7515264	0.80[AMR][1000 genomes]
rs7515976	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs7520283	0.90[JPT][hapmap]
rs7532712	0.80[AMR][1000 genomes]
rs903263	0.83[MEX][hapmap]
rs953197	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs957828	0.80[JPT][hapmap]
rs970318	0.81[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11163900	BCL10	cis	cerebellum	SCAN
rs11163900	PRKACB	cis	lymphoblastoid	seeQTL
rs11163900	MCOLN2	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84545000-84558800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:84545000-84560600	Weak transcription	Fetal Lung	lung
3	chr1:84545000-84561200	Weak transcription	Ovary	ovary
4	chr1:84545000-84566800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:84545000-84570000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:84545200-84568600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:84545400-84560800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:84545800-84568600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:84546400-84560400	Weak transcription	Dnd41	blood
10	chr1:84552200-84558600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:84552200-84561800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:84552200-84561800	Weak transcription	Right Atrium	heart
13	chr1:84552200-84569000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:84552600-84562000	Weak transcription	Fetal Stomach	stomach
15	chr1:84554600-84560000	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:84555400-84558200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:84555400-84559800	Weak transcription	NH-A	brain
18	chr1:84555400-84568400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:84556400-84557800	Weak transcription	HSMMtube	muscle
20	chr1:84556400-84559600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:84556400-84559800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:84556400-84568400	Weak transcription	Brain Angular Gyrus	brain
23	chr1:84556400-84568400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:84556400-84568400	Weak transcription	A549	lung
25	chr1:84556400-84568400	Weak transcription	HSMM	muscle
26	chr1:84556400-84569000	Weak transcription	Left Ventricle	heart
27	chr1:84556600-84561000	Weak transcription	HMEC	breast
28	chr1:84556600-84566400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:84556600-84566600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:84556600-84568600	Weak transcription	Brain Substantia Nigra	brain
31	chr1:84556800-84557600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:84556800-84557600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr1:84556800-84560400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:84557000-84557600	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr1:84557000-84559200	Weak transcription	Fetal Intestine Small	intestine
36	chr1:84557200-84557600	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr1:84557200-84557600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr1:84557200-84557600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr1:84557200-84557600	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr1:84557200-84558000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:84557200-84558000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:84557200-84558400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr1:84557400-84557600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:84557400-84557600	Weak transcription	Gastric	stomach

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