Variant report

Variant	rs7580912
Chromosome Location	chr2:231081405-231081406
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	BCL11A	chr2:231081280-231081473	GM12878	blood:	n/a	n/a
2	RUNX3	chr2:231081231-231081647	GM12878	blood:	n/a	chr2:231081420-231081429 chr2:231081420-231081429 chr2:231081414-231081429
3	EBF1	chr2:231081302-231081558	GM12878	blood:	n/a	n/a
4	FOXM1	chr2:231081167-231081583	GM12878	blood:	n/a	n/a
5	BATF	chr2:231081292-231081652	GM12878	blood:	n/a	n/a
6	RUNX3	chr2:231081129-231081640	GM12878	blood:	n/a	chr2:231081420-231081429 chr2:231081420-231081429 chr2:231081414-231081429
7	IKZF1	chr2:231081223-231081555	GM12878	blood:	n/a	n/a
8	NFIC	chr2:231081072-231081688	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:231072082..231074333-chr2:231080031..231082815,2	MCF-7	breast:
2	chr2:231080762..231082857-chr2:231083207..231085642,2	K562	blood:

Variant related genes	Relation type
SP110	TF binding region
ENSG00000135899	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12477362	0.86[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs12690536	0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs16826955	0.87[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2288328	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60232929	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6709625	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6720816	0.86[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs7573954	0.86[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7578826	0.88[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs9288662	0.81[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs9288663	0.86[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv869834	chr2:231045013-231139827	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv998291	chr2:231045388-231136278	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv584666	chr2:231050715-231106621	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231059000-231082800	Weak transcription	Stomach Mucosa	stomach
2	chr2:231062200-231081600	Strong transcription	Liver	Liver
3	chr2:231062400-231081600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:231062600-231081600	Strong transcription	Fetal Lung	lung
5	chr2:231062600-231081600	Strong transcription	Placenta	Placenta
6	chr2:231062600-231081600	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr2:231062600-231081600	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:231062600-231081800	Strong transcription	Fetal Muscle Trunk	muscle
9	chr2:231062600-231082200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:231062600-231082400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:231062600-231084200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:231063000-231084000	Weak transcription	Hela-S3	cervix
13	chr2:231063200-231084000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:231063400-231082200	Strong transcription	Fetal Muscle Leg	muscle
15	chr2:231064800-231084000	Weak transcription	Fetal Heart	heart
16	chr2:231066200-231083200	Weak transcription	HUVEC	blood vessel
17	chr2:231066200-231084400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:231066400-231081600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:231067200-231081600	Strong transcription	Left Ventricle	heart
20	chr2:231067600-231084200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:231068200-231082200	Strong transcription	Ovary	ovary
22	chr2:231068200-231084400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:231068400-231081800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:231068400-231084000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:231069400-231081600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:231070200-231081600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:231070800-231081600	Strong transcription	Lung	lung
28	chr2:231071800-231084200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:231072400-231081600	Strong transcription	Fetal Stomach	stomach
30	chr2:231073200-231081600	Strong transcription	Right Ventricle	heart
31	chr2:231073600-231084000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr2:231074200-231084000	Weak transcription	Fetal Kidney	kidney
33	chr2:231074800-231081800	Strong transcription	Spleen	Spleen
34	chr2:231075200-231081800	Strong transcription	Thymus	Thymus
35	chr2:231075400-231082000	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:231076000-231081800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr2:231076000-231084200	Weak transcription	Brain Angular Gyrus	brain
38	chr2:231076800-231081600	Strong transcription	Colon Smooth Muscle	Colon
39	chr2:231076800-231084000	Weak transcription	NHDF-Ad	bronchial
40	chr2:231077400-231084000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr2:231077400-231084000	Weak transcription	NH-A	brain
42	chr2:231077400-231084000	Weak transcription	Osteobl	bone
43	chr2:231077400-231084200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr2:231077600-231084000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:231077800-231082800	Weak transcription	HepG2	liver
46	chr2:231077800-231084000	Weak transcription	NHLF	lung
47	chr2:231078000-231082000	Weak transcription	Fetal Intestine Small	intestine
48	chr2:231078000-231082600	Weak transcription	Colonic Mucosa	Colon
49	chr2:231078000-231082600	Weak transcription	Psoas Muscle	Psoas
50	chr2:231078000-231084200	Weak transcription	Pancreas	Pancrea

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