Variant report

Variant	rs11125135
Chromosome Location	chr2:47619080-47619081
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	chr2:47616200..47619082-chr2:47621954..47624826,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11125134	0.84[ASN][1000 genomes]
rs11688368	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11692854	0.93[ASN][1000 genomes]
rs11695550	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34595241	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7584256	0.82[CEU][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11125135	MSH2	cis	Artery Tibial	GTEx
rs11125135	MSH2	cis	lung	GTEx
rs11125135	MSH2	cis	Artery Aorta	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47597200-47619800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:47597400-47629400	Weak transcription	NHEK	skin
3	chr2:47601200-47629400	Weak transcription	Stomach Mucosa	stomach
4	chr2:47604800-47628800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:47605200-47629000	Weak transcription	Brain Germinal Matrix	brain
6	chr2:47607800-47624000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:47608000-47629000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:47609200-47619600	Strong transcription	Fetal Intestine Large	intestine
9	chr2:47609800-47619600	Weak transcription	Gastric	stomach
10	chr2:47609800-47629200	Weak transcription	Fetal Stomach	stomach
11	chr2:47611800-47619400	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr2:47612000-47629000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:47613400-47619200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:47613800-47620800	Weak transcription	Fetal Kidney	kidney
15	chr2:47614000-47620400	Strong transcription	Fetal Intestine Small	intestine
16	chr2:47614000-47620800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:47614200-47628800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:47615000-47619200	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr2:47615600-47619400	Strong transcription	Duodenum Mucosa	Duodenum
20	chr2:47615600-47629400	Weak transcription	Colonic Mucosa	Colon
21	chr2:47616200-47623400	Weak transcription	HepG2	liver
22	chr2:47616800-47629200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:47617000-47629400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:47617200-47628800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:47617200-47629000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:47617400-47629600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:47617800-47619400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:47618200-47619400	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:47618800-47619400	Strong transcription	Pancreas	Pancrea
30	chr2:47619000-47619200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:47619000-47620000	Enhancers	K562	blood

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