Variant report

Variant	rs13424896
Chromosome Location	chr2:233756979-233756980
allele	C/T
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	chr2:233756798-233756997	HepG2	liver:	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: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10178713	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10207739	0.81[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap]
rs11679581	0.80[AMR][1000 genomes]
rs11684636	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs11694000	0.87[TSI][hapmap]
rs11904619	0.90[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12052869	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs12328140	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12328151	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12694915	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap]
rs12992588	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13012585	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13035517	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13383733	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13387762	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13390935	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13401578	0.86[CHB][hapmap]
rs13425918	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1446307	0.95[CEU][hapmap];0.84[CHB][hapmap]
rs2044450	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2048866	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289914	0.95[CEU][hapmap]
rs2289915	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs2292724	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2292725	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2293782	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs28491817	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34063802	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap]
rs34652626	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35141217	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62193305	0.80[AMR][1000 genomes]
rs6437073	0.81[TSI][hapmap]
rs6747479	0.89[CEU][hapmap]
rs6751801	0.81[TSI][hapmap]
rs73005582	0.80[AMR][1000 genomes]
rs9288675	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs9288676	0.94[CEU][hapmap];0.86[CHB][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

No data

Chromatin state (count:40 , 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	chr2:233753200-233757200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:233755400-233757000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:233755400-233757000	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr2:233755400-233759800	Strong transcription	Colonic Mucosa	Colon
12	chr2:233755600-233757000	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr2:233755600-233757000	Enhancers	HSMM	muscle
14	chr2:233755600-233757400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:233755600-233757400	Enhancers	Brain Angular Gyrus	brain
16	chr2:233755600-233757400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr2:233755600-233757800	Strong transcription	Gastric	stomach
18	chr2:233755600-233759400	Strong transcription	Fetal Intestine Small	intestine
19	chr2:233755800-233757000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:233755800-233757200	Enhancers	Brain Cingulate Gyrus	brain
21	chr2:233755800-233757200	Enhancers	Brain Hippocampus Middle	brain
22	chr2:233755800-233757400	Enhancers	Brain Anterior Caudate	brain
23	chr2:233756000-233757200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:233756000-233758200	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:233756200-233757000	Strong transcription	Fetal Brain Female	brain
26	chr2:233756200-233757000	Enhancers	Pancreas	Pancrea
27	chr2:233756200-233763600	Weak transcription	NHLF	lung
28	chr2:233756400-233757000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr2:233756400-233759200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr2:233756400-233763800	Weak transcription	Right Atrium	heart
31	chr2:233756600-233757800	Weak transcription	Spleen	Spleen
32	chr2:233756600-233763400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:233756600-233766400	Weak transcription	Brain Substantia Nigra	brain
34	chr2:233756800-233757000	Weak transcription	Esophagus	oesophagus
35	chr2:233756800-233757000	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr2:233756800-233757000	Enhancers	Osteobl	bone
37	chr2:233756800-233757200	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr2:233756800-233757200	Enhancers	HMEC	breast
39	chr2:233756800-233757400	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr2:233756800-233765400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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