Variant report

Variant	rs11891189
Chromosome Location	chr2:47737398-47737399
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47735627..47737590-chr2:47744199..47746815,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11675417	0.86[CHB][hapmap]
rs11677098	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12619323	0.84[ASN][1000 genomes]
rs13009248	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13031209	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17036614	0.83[ASN][1000 genomes]
rs17036639	0.93[ASN][1000 genomes]
rs2042649	0.85[ASN][1000 genomes]
rs3771283	0.82[ASN][1000 genomes]
rs6544993	0.93[ASN][1000 genomes]
rs6751501	0.85[CHB][hapmap]
rs7587143	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv998314	chr2:47720420-47959168	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11891189	MSH2	cis	Artery Tibial	GTEx
rs11891189	MSH2	cis	lung	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47732600-47747800	Weak transcription	Primary T cells from cord blood	blood
2	chr2:47733600-47739200	Weak transcription	Right Atrium	heart
3	chr2:47734000-47740800	Weak transcription	Brain Angular Gyrus	brain
4	chr2:47734000-47741000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:47734000-47741400	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:47734000-47747000	Weak transcription	Brain Anterior Caudate	brain
7	chr2:47734000-47747600	Weak transcription	Brain Substantia Nigra	brain
8	chr2:47734800-47738200	Enhancers	Fetal Brain Male	brain
9	chr2:47735400-47737400	Enhancers	Dnd41	blood
10	chr2:47735400-47738400	Enhancers	Fetal Brain Female	brain
11	chr2:47736800-47742800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:47736800-47747400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:47736800-47747400	Weak transcription	Thymus	Thymus
14	chr2:47737000-47747200	Weak transcription	GM12878-XiMat	blood
15	chr2:47737200-47739200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:47737200-47739600	Weak transcription	HUVEC	blood vessel
17	chr2:47737200-47741200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:47737200-47741200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:47737200-47743400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:47737200-47744400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:47737200-47744800	Weak transcription	Fetal Thymus	thymus

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