Variant report

Variant	rs670246
Chromosome Location	chr11:74690776-74690777
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	chr11:74670533..74672513-chr11:74690416..74693115,2	MCF-7	breast:
2	chr11:74687560..74690870-chr11:74698064..74700699,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162139	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11236255	0.82[ASN][1000 genomes]
rs11236291	0.81[JPT][hapmap]
rs11236292	0.81[JPT][hapmap]
rs1125609	0.94[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs113187	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11827626	0.88[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs12223829	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1282668	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1282675	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1282677	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1315299	0.87[ASN][1000 genomes]
rs1821352	0.81[ASN][1000 genomes]
rs1866562	0.88[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2510692	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs474445	0.81[ASN][1000 genomes]
rs483271	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs487207	0.81[ASN][1000 genomes]
rs487226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491826	0.86[ASN][1000 genomes]
rs493001	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs494474	0.88[CEU][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs4944962	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs496698	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs500827	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs503855	0.88[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.80[ASN][1000 genomes]
rs503994	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs507620	0.88[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs512782	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs514534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs516287	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs517035	0.88[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs517666	0.94[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs517939	0.89[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs528800	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs534595	0.80[ASN][1000 genomes]
rs535705	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs536412	0.81[JPT][hapmap]
rs536823	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs544115	0.81[JPT][hapmap]
rs544891	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs558303	0.86[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs559211	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs562581	0.83[ASN][1000 genomes]
rs565377	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs571437	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs578477	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs579581	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs580541	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs592045	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs605954	0.86[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs629191	0.84[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs633824	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs639768	0.81[JPT][hapmap]
rs650130	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs655488	0.88[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs662062	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs671544	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs673731	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs681566	0.82[CEU][hapmap];0.93[JPT][hapmap];0.82[TSI][hapmap]
rs685116	0.80[JPT][hapmap]
rs693212	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7121530	0.82[ASN][1000 genomes]
rs7128833	0.81[JPT][hapmap]
rs7952096	0.81[JPT][hapmap]
rs7952209	0.81[JPT][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	nsv832210	chr11:74562782-74732133	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs670246	XRRA1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74661800-74699200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:74661800-74699400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:74662200-74699600	Weak transcription	Esophagus	oesophagus
4	chr11:74662400-74691400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:74667800-74692200	Strong transcription	Dnd41	blood
6	chr11:74672000-74692000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:74673400-74691000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr11:74673400-74694400	Weak transcription	Stomach Mucosa	stomach
9	chr11:74673800-74691600	Strong transcription	Primary B cells from peripheral blood	blood
10	chr11:74674000-74692200	Strong transcription	GM12878-XiMat	blood
11	chr11:74674600-74692000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:74674600-74692000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:74674800-74692400	Strong transcription	Fetal Thymus	thymus
14	chr11:74675000-74692000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr11:74675000-74692200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr11:74675200-74691400	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr11:74675200-74691400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr11:74675200-74692200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:74675600-74692000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:74675600-74692200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:74675600-74699400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr11:74675800-74692200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr11:74676600-74691800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:74676600-74691800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:74677000-74691600	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr11:74677200-74691400	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr11:74677200-74692400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr11:74677200-74692400	Strong transcription	Fetal Muscle Leg	muscle
29	chr11:74677200-74692600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:74677200-74692600	Strong transcription	Thymus	Thymus
31	chr11:74677200-74693400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:74677600-74691200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr11:74677600-74693800	Strong transcription	HSMM	muscle
34	chr11:74678600-74699200	Weak transcription	Spleen	Spleen
35	chr11:74679800-74691600	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr11:74680200-74691000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr11:74680200-74691200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr11:74680200-74692200	Strong transcription	Primary T cells from cord blood	blood
39	chr11:74680400-74691400	Strong transcription	Placenta	Placenta
40	chr11:74680400-74691600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr11:74680400-74692400	Strong transcription	Fetal Brain Female	brain
42	chr11:74680600-74691600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:74681000-74692400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:74681000-74699200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr11:74681200-74699600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr11:74682200-74691400	Strong transcription	Lung	lung
47	chr11:74682200-74692200	Strong transcription	Fetal Intestine Large	intestine
48	chr11:74682800-74692400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr11:74682800-74692600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr11:74683000-74691600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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