Variant report

Variant	rs709937
Chromosome Location	chr2:233744021-233744022
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:233738116..233740416-chr2:233743291..233745431,2	K562	blood:
2	chr2:233739591..233745527-chr2:233747956..233752237,8	MCF-7	breast:
3	chr2:233741423..233744026-chr2:234158649..234161710,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085978	Chromatin interaction
ENSG00000182600	Chromatin interaction
ENSG00000066248	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1083522	0.85[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933406	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1104764	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12105766	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap]
rs12619195	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs13029336	0.83[JPT][hapmap]
rs1515961	0.83[JPT][hapmap]
rs1973675	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap]
rs2675953	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675954	0.85[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675968	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675972	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs283470	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs283473	0.83[JPT][hapmap]
rs4973564	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.94[ASN][1000 genomes]
rs4973569	0.87[CEU][hapmap]
rs6704763	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap]
rs6717048	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6733495	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs737027	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs748002	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778341	0.95[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs778370	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778371	0.85[EUR][1000 genomes]
rs938569	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs938575	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1009825	chr2:233709566-233763470	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv984452	chr2:233725452-233762965	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking 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	7 gene(s)	inside rSNPs	diseases
7	nsv999116	chr2:233733352-233759864	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1007029	chr2:233733352-233760519	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv536179	chr2:233735380-233757170	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs709937	TIGD1	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233726800-233755600	Weak transcription	HSMMtube	muscle
2	chr2:233741600-233745000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr2:233741600-233747000	Weak transcription	Gastric	stomach
4	chr2:233741600-233747600	Weak transcription	NHLF	lung
5	chr2:233741600-233749600	Weak transcription	Pancreas	Pancrea
6	chr2:233741800-233750000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:233742000-233749000	Weak transcription	Small Intestine	intestine
8	chr2:233742200-233745200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:233742200-233747400	Weak transcription	Fetal Brain Female	brain
10	chr2:233742200-233749800	Weak transcription	Brain Germinal Matrix	brain
11	chr2:233742200-233750000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:233742200-233750800	Weak transcription	Fetal Brain Male	brain
13	chr2:233742400-233745200	Enhancers	Brain Cingulate Gyrus	brain
14	chr2:233742400-233752400	Weak transcription	Colonic Mucosa	Colon
15	chr2:233742400-233754200	Strong transcription	Fetal Intestine Small	intestine
16	chr2:233742400-233755600	Weak transcription	Fetal Intestine Large	intestine
17	chr2:233742600-233744400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:233742600-233745800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:233742600-233753400	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr2:233742800-233744600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:233742800-233746000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:233742800-233755600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:233743000-233744200	Weak transcription	A549	lung
24	chr2:233743000-233744800	Strong transcription	Esophagus	oesophagus
25	chr2:233743000-233745000	Enhancers	Brain Anterior Caudate	brain
26	chr2:233743000-233748000	Weak transcription	Brain Substantia Nigra	brain
27	chr2:233743000-233753000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:233743000-233755800	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:233743200-233745800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:233743200-233746200	Genic enhancers	HepG2	liver
31	chr2:233743200-233759600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr2:233743800-233744600	Weak transcription	Brain Angular Gyrus	brain
33	chr2:233744000-233744200	Weak transcription	Liver	Liver

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