Variant report

Variant	rs2957873
Chromosome Location	chr11:47249294-47249295
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	chr11:47206928..47208678-chr11:47247799..47249316,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165912	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1051006	0.87[ASW][hapmap];0.82[MEX][hapmap]
rs10769253	0.82[MEX][hapmap]
rs10769255	0.82[MEX][hapmap]
rs10838663	0.81[MEX][hapmap]
rs10838687	0.94[ASW][hapmap];0.84[CEU][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs10838689	0.82[MEX][hapmap]
rs11039144	0.87[AMR][1000 genomes]
rs11039148	0.86[AMR][1000 genomes]
rs16938581	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2013867	0.81[CHD][hapmap]
rs2087215	0.81[MEX][hapmap]
rs2167079	0.81[CHD][hapmap]
rs2242261	0.94[ASW][hapmap];0.82[CHB][hapmap];0.88[LWK][hapmap];0.81[MEX][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2242262	0.82[CHB][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2279238	0.94[ASW][hapmap];0.82[MEX][hapmap];0.83[YRI][hapmap]
rs2290146	0.87[ASW][hapmap];0.82[YRI][hapmap]
rs2290148	0.87[ASW][hapmap];0.82[YRI][hapmap]
rs2305280	0.94[ASW][hapmap];0.86[YRI][hapmap]
rs2306353	0.82[CHB][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2596397	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2596398	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2633080	0.84[CHB][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2633082	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2633083	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs326222	0.81[CHD][hapmap]
rs326224	0.80[ASN][1000 genomes]
rs3758670	0.87[AMR][1000 genomes]
rs3758673	0.82[ASW][hapmap];0.81[CHD][hapmap];0.84[LWK][hapmap];0.85[MKK][hapmap];0.80[YRI][hapmap]
rs3781619	0.94[ASW][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.82[MEX][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3781620	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs3824866	0.82[CHB][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes]
rs4647725	0.95[AMR][1000 genomes]
rs4647726	0.95[AMR][1000 genomes]
rs4647737	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4647741	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4647754	0.87[AMR][1000 genomes]
rs4647757	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4752965	0.86[MEX][hapmap]
rs4752972	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4752973	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4752977	0.87[ASW][hapmap];0.86[YRI][hapmap]
rs4752983	0.94[ASW][hapmap];0.82[MEX][hapmap]
rs6485751	0.81[EUR][1000 genomes]
rs7118396	0.94[ASW][hapmap];0.82[CHB][hapmap];0.82[MEX][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes]
rs7120118	0.81[CHD][hapmap];0.80[YRI][hapmap]
rs7120158	0.82[CHB][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7124958	0.81[YRI][hapmap]
rs7395496	0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs7395581	0.82[ASW][hapmap];0.81[CHB][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes]
rs753992	0.82[MEX][hapmap]
rs753993	0.84[CEU][hapmap]
rs7933246	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7947269	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7950753	0.81[MEX][hapmap]
rs830083	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs830084	0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs830085	0.82[ASW][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes]
rs901746	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2957873	MTCH2	cis	cerebellum	SCAN
rs2957873	CYTSB	trans	parietal	SCAN
rs2957873	DDB2	cis	lymphoblastoid	seeQTL
rs2957873	ACP2	cis	lymphoblastoid	seeQTL
rs2957873	ACP2	cis	Thyroid	GTEx
rs2957873	ACP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47238400-47255800	Weak transcription	Brain Anterior Caudate	brain
2	chr11:47238400-47269400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:47238600-47253800	Weak transcription	Aorta	Aorta
4	chr11:47238600-47254200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:47238600-47255400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr11:47238600-47255400	Weak transcription	Right Ventricle	heart
7	chr11:47238600-47255600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr11:47238600-47255800	Weak transcription	Brain Substantia Nigra	brain
9	chr11:47238600-47255800	Weak transcription	Right Atrium	heart
10	chr11:47238600-47256000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr11:47238600-47259600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr11:47238600-47261000	Weak transcription	Small Intestine	intestine
13	chr11:47238800-47254000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:47239400-47252200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:47239400-47252200	Strong transcription	Fetal Thymus	thymus
16	chr11:47239400-47255000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr11:47239600-47251800	Strong transcription	Fetal Stomach	stomach
18	chr11:47239800-47254200	Weak transcription	Lung	lung
19	chr11:47239800-47255600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr11:47239800-47255600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr11:47240000-47252400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr11:47240000-47260200	Weak transcription	Fetal Brain Female	brain
23	chr11:47240200-47254200	Weak transcription	Esophagus	oesophagus
24	chr11:47240200-47254200	Weak transcription	Stomach Mucosa	stomach
25	chr11:47240200-47254600	Weak transcription	Pancreas	Pancrea
26	chr11:47240200-47255400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr11:47240200-47255600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr11:47240200-47255800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr11:47240200-47256000	Weak transcription	Gastric	stomach
30	chr11:47240200-47266600	Weak transcription	Fetal Brain Male	brain
31	chr11:47240400-47255800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:47241400-47255600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr11:47241800-47254400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr11:47241800-47256000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr11:47242000-47255800	Weak transcription	Left Ventricle	heart
36	chr11:47242200-47250600	Weak transcription	HSMMtube	muscle
37	chr11:47242200-47255400	Weak transcription	Brain Hippocampus Middle	brain
38	chr11:47242200-47258200	Weak transcription	Fetal Lung	lung
39	chr11:47242400-47250600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:47242400-47254200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr11:47242400-47256000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr11:47242400-47257800	Weak transcription	K562	blood
43	chr11:47242400-47258000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:47242400-47258000	Weak transcription	Primary B cells from cord blood	blood
45	chr11:47242400-47269200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr11:47242600-47253200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:47242600-47259600	Weak transcription	Brain Germinal Matrix	brain
48	chr11:47242600-47260200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr11:47242800-47254200	Weak transcription	NHLF	lung
50	chr11:47242800-47255200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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