Variant report

Variant	rs1371410
Chromosome Location	chr11:74725298-74725299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74697161..74701589-chr11:74722600..74726344,4	K562	blood:
2	chr11:74723507..74725888-chr11:74813976..74816359,2	K562	blood:

Variant related genes	Relation type
ENSG00000162139	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10751241	0.91[CEU][hapmap];0.95[JPT][hapmap]
rs10793107	0.95[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10793108	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10899051	0.81[AMR][1000 genomes]
rs10899052	0.91[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs10899053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10899054	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899058	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899059	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10899060	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11236281	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236290	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236294	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11236296	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11600328	0.83[AFR][1000 genomes]
rs11603294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12221841	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs12577127	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[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12577614	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2119028	0.96[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2165162	0.96[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2165163	0.96[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2298746	0.92[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs2304683	0.92[CEU][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs3814726	0.86[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap]
rs4245440	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[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4387374	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[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4456280	0.90[GIH][hapmap]
rs4483614	0.92[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap]
rs4944960	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs4944961	0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap]
rs4944965	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944968	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56194145	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7105085	0.91[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs7109716	0.83[AFR][1000 genomes]
rs7128739	0.92[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs725460	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7396866	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7483351	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs919877	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs9787775	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9787897	0.81[AMR][1000 genomes];0.81[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:26)

SNP	Gene	Cis/trans	Tissue	Source
rs1371410	XRRA1	cis	Artery Tibial	GTEx
rs1371410	PLEKHB1	cis	cerebellum	SCAN
rs1371410	RP11-147I3.1	cis	Thyroid	GTEx
rs1371410	XRRA1	cis	Esophagus Muscularis	GTEx
rs1371410	XRRA1	cis	normal skin	skin_eQTL
rs1371410	XRRA1	cis	lymphoblastoid	seeQTL
rs1371410	XRRA1	cis	Adipose Subcutaneous	GTEx
rs1371410	XRRA1	cis	parietal	SCAN
rs1371410	RP11-147I3.1	cis	Muscle Skeletal	GTEx
rs1371410	RNF169	cis	lymphoblastoid	seeQTL
rs1371410	XRRA1	cis	Nerve Tibial	GTEx
rs1371410	XRRA1	cis	Stomach	GTEx
rs1371410	XRRA1	cis	Thyroid	GTEx
rs1371410	XRRA1	cis	Heart Left Ventricle	GTEx
rs1371410	XRRA1	cis	Muscle Skeletal	GTEx
rs1371410	XRRA1	cis	lesional skin	skin_eQTL
rs1371410	XRRA1	cis	lung	GTEx
rs1371410	XRRA1	cis	cerebellum	SCAN
rs1371410	PAAF1	cis	parietal	SCAN
rs1371410	XRRA1	cis	lymphoblastoid	GTEx
rs1371410	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs1371410	RNF169	cis	cerebellum	SCAN
rs1371410	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs1371410	XRRA1	cis	Whole Blood	GTEx
rs1371410	XRRA1	cis	Artery Aorta	GTEx
rs1371410	XRRA1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74712000-74728200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr11:74714200-74725400	Strong transcription	Dnd41	blood
3	chr11:74715600-74725400	Strong transcription	Liver	Liver
4	chr11:74716200-74725600	Strong transcription	Primary T cells from cord blood	blood
5	chr11:74716400-74725600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:74716400-74725600	Strong transcription	Thymus	Thymus
7	chr11:74717600-74725400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:74717600-74726000	Weak transcription	Esophagus	oesophagus
9	chr11:74718000-74733800	Weak transcription	Brain Substantia Nigra	brain
10	chr11:74718000-74734200	Weak transcription	Right Ventricle	heart
11	chr11:74718200-74726200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:74718200-74726200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:74718200-74729200	Weak transcription	Gastric	stomach
14	chr11:74718400-74726200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:74718400-74729800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr11:74718600-74725800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr11:74718800-74726600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr11:74719400-74728600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr11:74720400-74725400	Weak transcription	NH-A	brain
20	chr11:74721000-74726200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr11:74721600-74725400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr11:74721600-74726200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr11:74721600-74733400	Weak transcription	Pancreas	Pancrea
24	chr11:74721600-74734200	Weak transcription	Brain Angular Gyrus	brain
25	chr11:74721600-74734200	Weak transcription	Brain Anterior Caudate	brain
26	chr11:74721600-74734200	Weak transcription	Brain Hippocampus Middle	brain
27	chr11:74721600-74734200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr11:74721600-74734200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:74721800-74726000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr11:74721800-74728400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr11:74721800-74729400	Weak transcription	Fetal Intestine Small	intestine
32	chr11:74722000-74725800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr11:74722800-74725600	Strong transcription	Primary B cells from cord blood	blood
34	chr11:74722800-74730200	Weak transcription	Fetal Intestine Large	intestine
35	chr11:74723400-74730200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr11:74723600-74725600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr11:74723600-74725600	Enhancers	K562	blood
38	chr11:74723600-74729400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr11:74723600-74731800	Weak transcription	Left Ventricle	heart
40	chr11:74723800-74725600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:74723800-74725800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr11:74723800-74726200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr11:74723800-74729200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr11:74723800-74733800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr11:74724000-74725400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr11:74724000-74725600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr11:74724000-74725600	Enhancers	NHDF-Ad	bronchial
48	chr11:74724000-74725800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:74724000-74725800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:74724000-74725800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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