Variant report

Variant	rs2850437
Chromosome Location	chr11:102346088-102346089
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	chr11:102323431..102326231-chr11:102344415..102346737,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255337	Chromatin interaction
ENSG00000152558	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10750642	0.98[ASN][1000 genomes]
rs10750643	0.98[ASN][1000 genomes]
rs10791576	0.98[ASN][1000 genomes]
rs1941510	0.98[ASN][1000 genomes]
rs2186992	0.94[ASN][1000 genomes]
rs3990027	0.98[ASN][1000 genomes]
rs4754045	0.97[ASN][1000 genomes]
rs480950	0.92[ASW][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes]
rs488324	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs514188	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs541877	0.80[EUR][1000 genomes]
rs555650	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs562383	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs599384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603608	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs634743	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs634814	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs636898	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs650423	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs651319	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs653586	0.90[ASN][1000 genomes]
rs6590964	0.98[ASN][1000 genomes]
rs6590966	0.94[ASN][1000 genomes]
rs6590967	0.91[ASN][1000 genomes]
rs659789	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs665124	0.94[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs668660	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs938598	0.97[ASN][1000 genomes]
rs938600	0.95[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3514195	chr11:102118479-102348362	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv3514197	chr11:102118479-102348362	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1035567	chr11:102264516-102431607	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv898334	chr11:102272884-102353192	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv469990	chr11:102335609-102413943	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv556150	chr11:102335609-102415859	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv468854	chr11:102336617-102413943	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv556151	chr11:102336617-102413943	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2850437	MMP7	cis	parietal	SCAN
rs2850437	TMEM123	Cis_1M	lymphoblastoid	RTeQTL
rs2850437	PDGFD	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102338000-102347000	Weak transcription	Small Intestine	intestine
2	chr11:102339000-102347400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr11:102339800-102347000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:102340600-102346800	Weak transcription	A549	lung
5	chr11:102340800-102347000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr11:102340800-102347200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr11:102340800-102347600	Weak transcription	Lung	lung
8	chr11:102341000-102346800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr11:102341000-102347400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr11:102341000-102359600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:102341800-102347200	Weak transcription	Dnd41	blood
12	chr11:102342000-102347000	Weak transcription	Thymus	Thymus
13	chr11:102342000-102347200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr11:102342000-102347400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr11:102342000-102347400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr11:102342000-102347400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:102342000-102347400	Weak transcription	Fetal Heart	heart
18	chr11:102342400-102347000	Weak transcription	NHEK	skin
19	chr11:102342400-102347200	Weak transcription	Fetal Thymus	thymus
20	chr11:102342400-102347400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr11:102342400-102347400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr11:102342600-102346800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr11:102342800-102347000	Weak transcription	HMEC	breast
24	chr11:102342800-102347200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr11:102343000-102346200	Weak transcription	Liver	Liver
26	chr11:102344400-102346200	Enhancers	Primary B cells from cord blood	blood
27	chr11:102344400-102346800	Enhancers	HepG2	liver
28	chr11:102344600-102347000	Weak transcription	K562	blood
29	chr11:102344600-102348000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:102344600-102348200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:102345000-102346200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr11:102345000-102346200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr11:102345000-102347000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr11:102345000-102347200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr11:102345000-102347200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr11:102345000-102349200	Weak transcription	Colonic Mucosa	Colon
37	chr11:102345000-102351600	Weak transcription	Gastric	stomach
38	chr11:102345200-102346400	Weak transcription	Hela-S3	cervix
39	chr11:102345200-102346800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr11:102345200-102347000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr11:102345200-102347000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr11:102345200-102347000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr11:102345400-102346800	Weak transcription	Primary T cells from cord blood	blood
44	chr11:102345400-102347200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:102345400-102347400	Weak transcription	Fetal Lung	lung
46	chr11:102345600-102346800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr11:102345600-102346800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr11:102345600-102347000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr11:102345600-102347000	Weak transcription	Colon Smooth Muscle	Colon
50	chr11:102345600-102347000	Weak transcription	Stomach Mucosa	stomach

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