Variant report

Variant	rs4147547
Chromosome Location	chr4:100127311-100127312
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10000357	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10009145	0.88[CEU][hapmap];0.85[YRI][hapmap]
rs10015824	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10020052	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10030920	1.00[ASN][1000 genomes]
rs1154404	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1154415	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[TSI][hapmap]
rs11724783	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1311621	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs13121905	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13148577	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17595102	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap]
rs1800760	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1869458	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.84[TSI][hapmap]
rs1893883	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2000864	1.00[ASN][1000 genomes]
rs2187483	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851275	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[TSI][hapmap]
rs2851301	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[TSI][hapmap]
rs28720150	1.00[ASN][1000 genomes]
rs28762430	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28805070	0.96[ASN][1000 genomes]
rs28848249	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2903166	1.00[ASN][1000 genomes]
rs34195655	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34511427	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3857224	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4147544	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4147545	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4148886	0.83[ASN][1000 genomes]
rs4333190	1.00[ASN][1000 genomes]
rs4577585	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4585310	1.00[ASN][1000 genomes]
rs4699733	1.00[CHB][hapmap]
rs62325498	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6833176	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307238	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9994326	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];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
rs4147547	NHEDC2	cis	parietal	SCAN

Chromatin state (count:35 , 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	chr4:100115200-100129800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr4:100120600-100127600	Enhancers	Fetal Intestine Small	intestine
4	chr4:100123000-100127600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:100123800-100128200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:100124600-100128600	Weak transcription	Fetal Muscle Leg	muscle
7	chr4:100125600-100127600	Enhancers	NHDF-Ad	bronchial
8	chr4:100125800-100127600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:100125800-100127600	Enhancers	Fetal Intestine Large	intestine
10	chr4:100126000-100127400	Enhancers	Fetal Kidney	kidney
11	chr4:100126000-100127400	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr4:100126000-100130200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr4:100126200-100127600	Enhancers	Duodenum Mucosa	Duodenum
14	chr4:100126200-100127600	Flanking Active TSS	Fetal Lung	lung
15	chr4:100126600-100128600	Enhancers	Liver	Liver
16	chr4:100126800-100127600	Genic enhancers	HepG2	liver
17	chr4:100126800-100128000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:100126800-100128400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:100126800-100128600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:100127000-100128200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:100127000-100128200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr4:100127000-100128200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:100127000-100129600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:100127000-100129800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:100127000-100129800	Weak transcription	Aorta	Aorta
26	chr4:100127000-100129800	Weak transcription	NHLF	lung
27	chr4:100127000-100130600	Weak transcription	HSMMtube	muscle
28	chr4:100127000-100131000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:100127000-100131200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:100127000-100139000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr4:100127000-100139400	Weak transcription	Ovary	ovary
32	chr4:100127000-100140200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:100127000-100142600	Weak transcription	Small Intestine	intestine
34	chr4:100127200-100127400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr4:100127200-100128800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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