Variant report

Variant	rs11695550
Chromosome Location	chr2:47603660-47603661
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47602208..47603999-chr2:47614007..47616997,2	MCF-7	breast:
2	chr2:47575625..47578501-chr2:47601748..47604083,2	MCF-7	breast:
3	chr2:47559485..47574826-chr2:47594341..47605593,65	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234690	Chromatin interaction
ENSG00000119888	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11125134	0.87[ASN][1000 genomes]
rs11125135	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11688368	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11692854	0.88[ASN][1000 genomes]
rs34595241	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1009586	chr2:47552706-47621487	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11695550	MSH2	cis	Artery Tibial	GTEx
rs11695550	MSH2	cis	Nerve Tibial	GTEx
rs11695550	MSH2	cis	Artery Aorta	GTEx
rs11695550	MSH2	cis	lung	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47597200-47610600	Weak transcription	Right Atrium	heart
2	chr2:47597200-47615000	Weak transcription	Esophagus	oesophagus
3	chr2:47597200-47619800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:47597400-47604000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:47597400-47607000	Weak transcription	Gastric	stomach
6	chr2:47597400-47614800	Weak transcription	HMEC	breast
7	chr2:47597400-47617000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:47597400-47629400	Weak transcription	NHEK	skin
9	chr2:47597600-47615400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:47598400-47604200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:47598600-47604200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:47598600-47607000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:47598600-47607000	Weak transcription	Pancreas	Pancrea
14	chr2:47598600-47607200	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:47598600-47613000	Weak transcription	Lung	lung
16	chr2:47599000-47606200	Weak transcription	Fetal Kidney	kidney
17	chr2:47599200-47608000	Weak transcription	Fetal Stomach	stomach
18	chr2:47599400-47603800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:47600200-47617800	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:47600400-47616800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:47600600-47614000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:47600600-47617200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:47600800-47614000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:47601000-47604200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:47601000-47610200	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr2:47601000-47610600	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr2:47601000-47614200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:47601200-47604400	Weak transcription	Colonic Mucosa	Colon
29	chr2:47601200-47609400	Weak transcription	Brain Anterior Caudate	brain
30	chr2:47601200-47614600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:47601200-47616800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:47601200-47629400	Weak transcription	Stomach Mucosa	stomach
33	chr2:47601400-47610400	Weak transcription	Fetal Lung	lung
34	chr2:47601600-47607000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:47601600-47607800	Strong transcription	HepG2	liver
36	chr2:47601800-47605800	Strong transcription	Fetal Intestine Small	intestine
37	chr2:47602000-47607200	Weak transcription	Fetal Brain Male	brain
38	chr2:47602600-47605600	Strong transcription	Fetal Intestine Large	intestine
39	chr2:47602600-47610200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:47602800-47603800	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr2:47602800-47604800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr2:47602800-47605400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr2:47602800-47607400	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:47603200-47619000	Weak transcription	K562	blood
45	chr2:47603600-47604200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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