Variant report

Variant	rs2712819
Chromosome Location	chr11:74866107-74866108
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	chr11:74864381..74867462-chr11:74869783..74873226,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137491	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11236323	0.85[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs11236325	0.82[CEU][hapmap]
rs11236359	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1789694	0.91[JPT][hapmap]
rs2187435	0.95[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2712781	0.81[EUR][1000 genomes]
rs2712787	0.89[CEU][hapmap]
rs2712789	0.85[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap]
rs2712805	0.95[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2712807	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2712810	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712820	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2712821	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2851064	0.92[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2851066	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2851073	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2851074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2851085	0.85[CEU][hapmap];0.81[CHD][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs2851094	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2851096	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2851102	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2851110	0.91[ASN][1000 genomes]
rs4146884	0.85[CEU][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap]
rs7122948	0.85[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs753171	0.86[EUR][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	nsv897919	chr11:74862391-74875501	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2712819	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs2712819	XRRA1	cis	lymphoblastoid	seeQTL
rs2712819	XRRA1	cis	multi-tissue	Pritchard
rs2712819	XRRA1	cis	parietal	SCAN
rs2712819	INPPL1	cis	parietal	SCAN
rs2712819	XRRA1	cis	cerebellum	SCAN
rs2712819	UCP2	cis	parietal	SCAN
rs2712819	P2RY2	cis	parietal	SCAN
rs2712819	PHOX2A	cis	parietal	SCAN
rs2712819	PGM2L1	cis	parietal	SCAN
rs2712819	RNF169	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74861200-74868400	Active TSS	Brain Hippocampus Middle	brain
2	chr11:74861600-74866200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:74861600-74867200	Active TSS	Brain Cingulate Gyrus	brain
4	chr11:74863600-74866200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:74863600-74885600	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:74864000-74866200	Active TSS	Stomach Smooth Muscle	stomach
7	chr11:74864200-74898400	Weak transcription	Esophagus	oesophagus
8	chr11:74864400-74866400	Genic enhancers	Fetal Intestine Small	intestine
9	chr11:74864600-74866800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:74864800-74866200	Weak transcription	Gastric	stomach
11	chr11:74864800-74867000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr11:74864800-74867000	Enhancers	HepG2	liver
13	chr11:74864800-74868600	Enhancers	Pancreas	Pancrea
14	chr11:74864800-74870400	Enhancers	Fetal Intestine Large	intestine
15	chr11:74865000-74872000	Enhancers	Placenta	Placenta
16	chr11:74865400-74866800	Enhancers	Colonic Mucosa	Colon
17	chr11:74865400-74866800	Enhancers	Left Ventricle	heart
18	chr11:74865400-74867600	Enhancers	Adipose Nuclei	Adipose
19	chr11:74865400-74867600	Enhancers	Fetal Muscle Trunk	muscle
20	chr11:74865400-74867600	Enhancers	Right Ventricle	heart
21	chr11:74865400-74868000	Enhancers	Fetal Muscle Leg	muscle
22	chr11:74865400-74868200	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr11:74865400-74868200	Enhancers	Stomach Mucosa	stomach
24	chr11:74865400-74868600	Enhancers	Fetal Stomach	stomach
25	chr11:74865400-74868800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:74865400-74868800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr11:74865600-74866200	Enhancers	Fetal Lung	lung
28	chr11:74865600-74866400	Active TSS	Brain Angular Gyrus	brain
29	chr11:74865600-74866400	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr11:74865600-74866400	Enhancers	Fetal Thymus	thymus
31	chr11:74865600-74866400	Enhancers	Small Intestine	intestine
32	chr11:74865800-74866400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:74865800-74866400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:74865800-74866400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr11:74865800-74866400	Enhancers	Ovary	ovary
36	chr11:74865800-74866400	Enhancers	Right Atrium	heart
37	chr11:74865800-74866400	Enhancers	Spleen	Spleen
38	chr11:74866000-74866200	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr11:74866000-74866200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:74866000-74866200	Flanking Active TSS	Lung	lung
41	chr11:74866000-74866200	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr11:74866000-74866400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr11:74866000-74866400	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr11:74866000-74866800	Weak transcription	Brain Anterior Caudate	brain
45	chr11:74866000-74867000	Enhancers	Liver	Liver
46	chr11:74866000-74867400	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr11:74866000-74869000	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr11:74866000-74869600	Weak transcription	Brain Substantia Nigra	brain

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