Variant report

Variant	rs7601062
Chromosome Location	chr2:47745525-47745526
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47743998..47746424-chr2:47747321..47749054,2	K562	blood:
2	chr2:47735627..47737590-chr2:47744199..47746815,2	MCF-7	breast:
3	chr2:47738547..47740217-chr2:47745164..47747197,2	K562	blood:
4	chr2:47738717..47741955-chr2:47744813..47746664,3	K562	blood:
5	chr2:47742968..47745561-chr2:47746454..47749350,4	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10188090	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10197011	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10209369	0.88[CEU][hapmap];0.89[CHB][hapmap];0.87[AMR][1000 genomes]
rs10495945	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11684661	0.80[AMR][1000 genomes]
rs11684737	0.83[AMR][1000 genomes]
rs11886591	0.86[CEU][hapmap]
rs11896864	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11901645	0.91[EUR][1000 genomes]
rs12712994	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2059520	0.90[TSI][hapmap]
rs2303424	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3771274	0.85[CEU][hapmap];0.84[CHD][hapmap];0.85[MEX][hapmap]
rs4550716	0.88[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes]
rs4583514	0.92[CEU][hapmap]
rs6718364	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6720555	0.86[AMR][1000 genomes]
rs6722911	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs6744097	0.84[CHD][hapmap]
rs6746426	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6759990	0.88[CEU][hapmap];0.89[CHB][hapmap];0.86[AMR][1000 genomes]
rs7599880	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs876936	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs876937	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs879722	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9784092	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[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	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
5	nsv817599	chr2:47738456-47961099	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	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
rs7601062	MSH2	cis	cerebellum	SCAN
rs7601062	SIX2	cis	parietal	SCAN

Chromatin state (count:38 , 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	chr2:47734000-47747000	Weak transcription	Brain Anterior Caudate	brain
3	chr2:47734000-47747600	Weak transcription	Brain Substantia Nigra	brain
4	chr2:47736800-47747400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:47736800-47747400	Weak transcription	Thymus	Thymus
6	chr2:47737000-47747200	Weak transcription	GM12878-XiMat	blood
7	chr2:47738400-47747200	Weak transcription	Brain Germinal Matrix	brain
8	chr2:47739200-47747600	Weak transcription	Pancreas	Pancrea
9	chr2:47740000-47747200	Weak transcription	Spleen	Spleen
10	chr2:47740400-47746600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr2:47741200-47747400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:47741600-47747400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:47741800-47745800	Weak transcription	Fetal Intestine Small	intestine
14	chr2:47742400-47747000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:47742600-47747000	Weak transcription	Brain Angular Gyrus	brain
16	chr2:47742800-47748400	Enhancers	Fetal Brain Male	brain
17	chr2:47743600-47747600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:47743600-47778200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:47743800-47747400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:47744200-47747400	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:47744400-47746600	Enhancers	Fetal Brain Female	brain
22	chr2:47744400-47747200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:47744400-47747200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:47744600-47746800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:47744600-47746800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:47744600-47747200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:47744800-47746600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:47744800-47746800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:47744800-47747400	Enhancers	Fetal Thymus	thymus
30	chr2:47744800-47752600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:47745000-47745800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:47745000-47746800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:47745200-47745600	Enhancers	Dnd41	blood
34	chr2:47745200-47747600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:47745200-47747600	Weak transcription	Ovary	ovary
36	chr2:47745200-47749400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:47745400-47745600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:47745400-47748200	Weak transcription	Aorta	Aorta

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