Variant report

Variant	rs681566
Chromosome Location	chr11:74700896-74700897
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74659109..74661906-chr11:74698267..74701116,3	K562	blood:
2	chr11:74700408..74702361-chr11:74702653..74705005,3	K562	blood:
3	chr11:74658459..74662580-chr11:74698519..74701644,8	MCF-7	breast:
4	chr11:74659008..74661915-chr11:74699636..74702523,6	MCF-7	breast:
5	chr11:74647585..74649948-chr11:74700186..74702806,2	K562	blood:

Variant related genes	Relation type
ENSG00000118363	Chromatin interaction
ENSG00000166435	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11236291	0.82[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs11236292	0.82[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs1125609	0.87[JPT][hapmap]
rs113187	0.93[JPT][hapmap];0.82[TSI][hapmap]
rs11827626	0.87[JPT][hapmap]
rs12287793	0.88[ASN][1000 genomes]
rs1866562	0.87[JPT][hapmap]
rs3018833	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs483271	0.93[JPT][hapmap]
rs487226	0.82[CEU][hapmap];0.93[JPT][hapmap];0.82[TSI][hapmap]
rs493001	0.82[CEU][hapmap];0.93[JPT][hapmap];0.82[TSI][hapmap]
rs494474	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944962	0.93[JPT][hapmap]
rs500827	0.93[JPT][hapmap]
rs503855	0.87[JPT][hapmap]
rs512782	0.93[JPT][hapmap]
rs514534	0.82[CEU][hapmap];0.93[JPT][hapmap]
rs516287	0.93[JPT][hapmap]
rs517666	0.93[JPT][hapmap];0.82[TSI][hapmap]
rs522808	0.89[ASN][1000 genomes]
rs536412	0.82[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs544115	0.82[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs544891	0.93[JPT][hapmap];0.82[TSI][hapmap]
rs551371	0.86[ASN][1000 genomes]
rs559211	0.87[JPT][hapmap];0.82[TSI][hapmap]
rs565377	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs566480	0.90[ASN][1000 genomes]
rs568310	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs578477	0.93[JPT][hapmap]
rs579581	0.93[JPT][hapmap]
rs58778107	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58972415	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59860682	0.90[ASN][1000 genomes]
rs605954	0.93[JPT][hapmap];0.82[TSI][hapmap]
rs629191	0.82[CEU][hapmap];0.93[JPT][hapmap];0.82[TSI][hapmap]
rs639768	0.82[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs650130	0.93[JPT][hapmap]
rs655488	0.87[JPT][hapmap]
rs662062	0.93[JPT][hapmap];0.82[TSI][hapmap]
rs670246	0.82[CEU][hapmap];0.93[JPT][hapmap];0.82[TSI][hapmap]
rs671544	0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs673731	0.87[JPT][hapmap]
rs674122	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs685116	0.82[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs693212	0.93[JPT][hapmap]
rs7128833	0.82[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs7939123	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7952096	0.89[CEU][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7952209	0.94[CEU][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs681566	XRRA1	cis	lymphoblastoid	seeQTL
rs681566	PAAF1	cis	cerebellum	SCAN
rs681566	XRRA1	cis	parietal	SCAN
rs681566	FCHSD2	cis	cerebellum	SCAN
rs681566	NEU3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74699200-74701000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr11:74699200-74701000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:74699200-74701000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:74699200-74701000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr11:74699200-74701000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr11:74699200-74701200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr11:74699200-74701200	Active TSS	GM12878-XiMat	blood
8	chr11:74699400-74701000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr11:74699400-74701000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr11:74699400-74701000	Active TSS	H1 Cell Line	embryonic stem cell
11	chr11:74699400-74701000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr11:74699400-74701000	Active TSS	Right Atrium	heart
13	chr11:74699400-74701200	Active TSS	A549	lung
14	chr11:74699600-74701000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr11:74699600-74701000	Active TSS	Colon Smooth Muscle	Colon
16	chr11:74700000-74701200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:74700200-74701000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr11:74700400-74701000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:74700400-74701000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr11:74700400-74701000	Flanking Active TSS	Liver	Liver
21	chr11:74700400-74701000	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr11:74700400-74701000	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr11:74700400-74701000	Flanking Active TSS	Fetal Intestine Small	intestine
24	chr11:74700400-74701000	Flanking Active TSS	Fetal Thymus	thymus
25	chr11:74700400-74701000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr11:74700400-74701000	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr11:74700400-74701000	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr11:74700400-74701200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:74700400-74701400	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr11:74700400-74701400	Flanking Active TSS	Hela-S3	cervix
31	chr11:74700400-74702200	Flanking Active TSS	Dnd41	blood
32	chr11:74700400-74702200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr11:74700400-74716400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:74700400-74723000	Weak transcription	Small Intestine	intestine
35	chr11:74700600-74701000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr11:74700600-74701000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr11:74700600-74701000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr11:74700600-74701000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr11:74700600-74701000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:74700600-74701000	Enhancers	Fetal Lung	lung
41	chr11:74700600-74701000	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr11:74700600-74701000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr11:74700600-74701000	Flanking Active TSS	Thymus	Thymus
44	chr11:74700600-74701200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr11:74700600-74701200	Enhancers	Primary B cells from peripheral blood	blood
46	chr11:74700600-74701200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr11:74700600-74701400	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr11:74700600-74701400	Weak transcription	Pancreas	Pancrea
49	chr11:74700600-74701600	Flanking Active TSS	HepG2	liver
50	chr11:74700600-74701600	Flanking Active TSS	NHEK	skin

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