Variant report

Variant	rs2851071
Chromosome Location	chr11:74865716-74865717
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: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10899075	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1676878	0.85[AFR][1000 genomes]
rs1944616	0.83[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2018251	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2156656	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2465290	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2712786	0.85[JPT][hapmap]
rs2712788	0.85[JPT][hapmap]
rs2712793	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2712795	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2712797	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2712799	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2712800	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2712801	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2712802	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2712806	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2712808	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712811	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];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712814	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2712815	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2712816	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2712817	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2712818	0.89[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2851065	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2851067	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2851068	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2851069	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2851070	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851072	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.84[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]
rs2851075	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2851078	0.85[JPT][hapmap]
rs2851079	0.92[JPT][hapmap]
rs2851080	0.84[JPT][hapmap]
rs2851081	0.85[JPT][hapmap]
rs2851082	0.85[JPT][hapmap]
rs2851084	0.92[JPT][hapmap]
rs2851086	0.85[JPT][hapmap]
rs2851093	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2851095	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2851097	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2851103	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2851104	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2851105	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2851109	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2851112	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4335576	0.85[JPT][hapmap]
rs4435030	0.91[ASW][hapmap];0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap]
rs4944067	0.85[JPT][hapmap]
rs7117575	0.82[ASW][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap]
rs7121374	0.85[JPT][hapmap]
rs870505	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs870506	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs875482	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2851071	INPPL1	cis	parietal	SCAN
rs2851071	RNF169	cis	cerebellum	SCAN
rs2851071	XRRA1	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74861200-74868400	Active TSS	Brain Hippocampus Middle	brain
2	chr11:74861400-74866000	Active TSS	Brain Anterior Caudate	brain
3	chr11:74861600-74866200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:74861600-74867200	Active TSS	Brain Cingulate Gyrus	brain
5	chr11:74862200-74866000	Active TSS	Brain Substantia Nigra	brain
6	chr11:74863600-74866000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:74863600-74866000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr11:74863600-74866200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:74863600-74885600	Weak transcription	Colon Smooth Muscle	Colon
10	chr11:74864000-74866200	Active TSS	Stomach Smooth Muscle	stomach
11	chr11:74864200-74898400	Weak transcription	Esophagus	oesophagus
12	chr11:74864400-74865800	Weak transcription	Ovary	ovary
13	chr11:74864400-74866400	Genic enhancers	Fetal Intestine Small	intestine
14	chr11:74864600-74866800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:74864800-74865800	Weak transcription	Spleen	Spleen
16	chr11:74864800-74866200	Weak transcription	Gastric	stomach
17	chr11:74864800-74867000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr11:74864800-74867000	Enhancers	HepG2	liver
19	chr11:74864800-74868600	Enhancers	Pancreas	Pancrea
20	chr11:74864800-74870400	Enhancers	Fetal Intestine Large	intestine
21	chr11:74865000-74865800	Weak transcription	Right Atrium	heart
22	chr11:74865000-74872000	Enhancers	Placenta	Placenta
23	chr11:74865400-74866800	Enhancers	Colonic Mucosa	Colon
24	chr11:74865400-74866800	Enhancers	Left Ventricle	heart
25	chr11:74865400-74867600	Enhancers	Adipose Nuclei	Adipose
26	chr11:74865400-74867600	Enhancers	Fetal Muscle Trunk	muscle
27	chr11:74865400-74867600	Enhancers	Right Ventricle	heart
28	chr11:74865400-74868000	Enhancers	Fetal Muscle Leg	muscle
29	chr11:74865400-74868200	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr11:74865400-74868200	Enhancers	Stomach Mucosa	stomach
31	chr11:74865400-74868600	Enhancers	Fetal Stomach	stomach
32	chr11:74865400-74868800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:74865400-74868800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr11:74865600-74865800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:74865600-74865800	Flanking Active TSS	Lung	lung
36	chr11:74865600-74866000	Flanking Active TSS	Liver	Liver
37	chr11:74865600-74866000	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr11:74865600-74866000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr11:74865600-74866000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr11:74865600-74866000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr11:74865600-74866000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
42	chr11:74865600-74866200	Enhancers	Fetal Lung	lung
43	chr11:74865600-74866400	Active TSS	Brain Angular Gyrus	brain
44	chr11:74865600-74866400	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr11:74865600-74866400	Enhancers	Fetal Thymus	thymus
46	chr11:74865600-74866400	Enhancers	Small Intestine	intestine

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