Variant report

Variant	rs748002
Chromosome Location	chr2:233757679-233757680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:233757210-233758017	HepG2	liver:	n/a	n/a
2	CREB1	chr2:233757527-233757881	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:233744358..233746968-chr2:233756848..233759131,3	K562	blood:
2	chr2:233744737..233747188-chr2:233755867..233757866,2	MCF-7	breast:

Variant related genes	Relation type
NGEF	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1083522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[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	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[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];0.83[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];0.83[MEX][hapmap]
rs2675953	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675955	0.82[EUR][1000 genomes]
rs2675968	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];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675972	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];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs4973569	0.91[CEU][hapmap];0.80[TSI][hapmap]
rs6704763	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs6717048	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6733495	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs709937	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]
rs737027	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs778341	0.91[CEU][hapmap];0.85[TSI][hapmap]
rs778370	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];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs938569	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs938575	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs748002	TIGD1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233743200-233759600	Strong transcription	Duodenum Mucosa	Duodenum
2	chr2:233745600-233759800	Strong transcription	Liver	Liver
3	chr2:233749400-233766000	Weak transcription	A549	lung
4	chr2:233750600-233759800	Strong transcription	HepG2	liver
5	chr2:233750800-233761000	Weak transcription	Stomach Mucosa	stomach
6	chr2:233751000-233766000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:233751200-233758400	Weak transcription	Fetal Brain Male	brain
8	chr2:233755400-233759800	Strong transcription	Colonic Mucosa	Colon
9	chr2:233755600-233757800	Strong transcription	Gastric	stomach
10	chr2:233755600-233759400	Strong transcription	Fetal Intestine Small	intestine
11	chr2:233756000-233758200	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:233756200-233763600	Weak transcription	NHLF	lung
13	chr2:233756400-233759200	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr2:233756400-233763800	Weak transcription	Right Atrium	heart
15	chr2:233756600-233757800	Weak transcription	Spleen	Spleen
16	chr2:233756600-233763400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:233756600-233766400	Weak transcription	Brain Substantia Nigra	brain
18	chr2:233756800-233765400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:233757000-233759000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:233757000-233759400	Strong transcription	Esophagus	oesophagus
21	chr2:233757000-233765400	Weak transcription	Pancreas	Pancrea
22	chr2:233757000-233766200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:233757000-233766200	Weak transcription	Fetal Brain Female	brain
24	chr2:233757000-233766400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:233757200-233760200	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:233757200-233763400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr2:233757400-233758200	Weak transcription	Brain Anterior Caudate	brain
28	chr2:233757400-233759800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:233757400-233776600	Weak transcription	Brain Angular Gyrus	brain
30	chr2:233757600-233763400	Weak transcription	Rectal Mucosa Donor 31	rectum

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