Variant report

Variant	rs2000864
Chromosome Location	chr4:100123776-100123777
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10000357	0.92[ASN][1000 genomes]
rs10015824	0.85[ASN][1000 genomes]
rs10020052	0.92[ASN][1000 genomes]
rs10030920	1.00[ASN][1000 genomes]
rs1154404	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1154415	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs11724783	0.92[ASN][1000 genomes]
rs1311621	1.00[JPT][hapmap]
rs13121905	0.96[ASN][1000 genomes]
rs13148577	0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17595102	1.00[JPT][hapmap]
rs1800760	0.83[ASN][1000 genomes]
rs1869458	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs1893883	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2187483	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851275	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2851301	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs28720150	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28762430	1.00[ASN][1000 genomes]
rs28805070	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28848249	0.85[ASN][1000 genomes]
rs2903166	1.00[ASN][1000 genomes]
rs34195655	0.85[ASN][1000 genomes]
rs34511427	0.96[ASN][1000 genomes]
rs3857224	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs4147544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147545	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[ASN][1000 genomes]
rs4147547	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs4148886	0.83[ASN][1000 genomes]
rs4333190	1.00[ASN][1000 genomes]
rs4577585	0.96[ASN][1000 genomes]
rs4585310	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699733	1.00[CHB][hapmap]
rs62325498	0.92[ASN][1000 genomes]
rs6833176	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307238	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9994326	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1002574	chr4:100023999-100133693	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3355763	chr4:100070566-100376814	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv879657	chr4:100082154-100139366	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1014237	chr4:100102701-100365700	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1010988	chr4:100105463-100444445	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1000659	chr4:100117276-100444445	Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv999549	chr4:100121609-100351749	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv879658	chr4:100123776-100131163	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2000864	NFKB1	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100108400-100141600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:100114200-100126400	Weak transcription	Aorta	Aorta
3	chr4:100115200-100129800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:100120200-100124000	Enhancers	HepG2	liver
5	chr4:100120600-100124600	Enhancers	Fetal Intestine Large	intestine
6	chr4:100120600-100127600	Enhancers	Fetal Intestine Small	intestine
7	chr4:100121400-100124200	Enhancers	Liver	Liver
8	chr4:100121600-100126200	Enhancers	Fetal Lung	lung
9	chr4:100122600-100127000	Enhancers	Adipose Nuclei	Adipose
10	chr4:100122800-100124200	Enhancers	Stomach Mucosa	stomach
11	chr4:100122800-100124400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:100123000-100123800	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr4:100123000-100124000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:100123000-100124000	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr4:100123000-100125200	Enhancers	NHDF-Ad	bronchial
16	chr4:100123000-100127600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:100123200-100124000	Enhancers	Fetal Kidney	kidney
18	chr4:100123200-100124200	Enhancers	Duodenum Mucosa	Duodenum
19	chr4:100123200-100124400	Enhancers	NHLF	lung
20	chr4:100123400-100123800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:100123400-100124400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:100123400-100124400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr4:100123400-100124600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:100123400-100124600	Enhancers	Ovary	ovary
25	chr4:100123400-100124600	Enhancers	Small Intestine	intestine
26	chr4:100123400-100126400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr4:100123600-100126400	Weak transcription	Muscle Satellite Cultured Cells	--

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