Variant report

Variant	rs7730004
Chromosome Location	chr5:43191033-43191034
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	ZNF143	chr5:43190978-43191209	Hela-S3	cervix:	n/a	n/a
2	REST	chr5:43190914-43191149	K562	blood:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
3	REST	chr5:43190794-43191285	HCT-116	colon:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
4	REST	chr5:43190874-43191314	HCT-116	colon:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
5	REST	chr5:43190875-43191230	SK-N-SH	brain:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
6	REST	chr5:43190936-43191111	HepG2	liver:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
7	MYC	chr5:43191013-43191161	NB4	blood:	n/a	n/a
8	RCOR1	chr5:43190973-43191187	Hela-S3	cervix:	n/a	n/a
9	REST	chr5:43190824-43191280	GM12878	blood:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
10	REST	chr5:43190811-43191290	PFSK-1	brain:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
11	REST	chr5:43190868-43191337	U87	brain:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
12	REST	chr5:43190741-43191333	Hela-S3	cervix:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
13	REST	chr5:43190703-43191467	MCF-7	breast:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
14	REST	chr5:43190555-43191402	PFSK-1	brain:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
15	REST	chr5:43190919-43191109	GM12878	blood:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
16	SIN3AK20	chr5:43190950-43191100	PFSK-1	brain:	n/a	n/a
17	REST	chr5:43190932-43191168	PANC-1	pancreas:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
18	REST	chr5:43190620-43191352	PANC-1	pancreas:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
19	REST	chr5:43190784-43191291	HepG2	liver:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
20	REST	chr5:43190868-43191335	U87	brain:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
21	TEAD4	chr5:43190921-43191219	A549	lung:	n/a	n/a
22	SIN3A	chr5:43190944-43191219	H1-hESC	embryonic stem cell:	n/a	chr5:43191034-43191047 chr5:43191038-43191048 chr5:43191033-43191041
23	REST	chr5:43190891-43191129	GM12878	blood:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
24	REST	chr5:43190838-43191345	HL-60	blood:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
25	ZNF143	chr5:43190972-43191167	GM12878	blood:	n/a	n/a
26	REST	chr5:43190662-43191430	A549	lung:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
27	REST	chr5:43190876-43191259	H1-hESC	embryonic stem cell:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
28	REST	chr5:43190811-43191306	SK-N-SH	brain:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
29	REST	chr5:43190806-43191283	PFSK-1	brain:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
30	REST	chr5:43190598-43191507	ECC-1	luminal epithelium:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
31	REST	chr5:43190888-43191252	HepG2	liver:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
32	REST	chr5:43190581-43191601	ECC-1	luminal epithelium:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
33	REST	chr5:43190922-43191150	GM12878	blood:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
34	REST	chr5:43190830-43191262	A549	lung:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
35	REST	chr5:43190764-43191306	MCF-7	breast:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
36	REST	chr5:43190928-43191173	HepG2	liver:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
37	REST	chr5:43190885-43191179	PFSK-1	brain:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
38	REST	chr5:43190808-43191257	K562	blood:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
39	REST	chr5:43190876-43191297	PANC-1	pancreas:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
40	REST	chr5:43190550-43191744	HL-60	blood:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
41	REST	chr5:43190928-43191163	PANC-1	pancreas:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
42	REST	chr5:43190756-43191442	PANC-1	pancreas:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
43	REST	chr5:43190908-43191230	U87	brain:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
44	REST	chr5:43190911-43191154	SK-N-SH	brain:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
45	REST	chr5:43190871-43191250	H1-hESC	embryonic stem cell:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043
46	REST	chr5:43190853-43191251	Hela-S3	cervix:	n/a	chr5:43191039-43191048 chr5:43191034-43191047 chr5:43191034-43191054 chr5:43191034-43191043

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43189592..43191167-chr5:43199369..43202364,2	K562	blood:

Variant related genes	Relation type
NIM1K	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10041458	0.82[ASN][1000 genomes]
rs10044382	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10058350	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10058374	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10070751	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10074873	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10075647	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10076858	0.85[EUR][1000 genomes]
rs10078527	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs10214190	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10805667	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10941607	0.87[JPT][hapmap]
rs10941608	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs10941611	0.86[ASN][1000 genomes]
rs11550287	0.87[JPT][hapmap]
rs11740797	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs11748187	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs13173064	0.87[JPT][hapmap]
rs13176429	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13665	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1532330	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1532331	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17301375	0.94[JPT][hapmap]
rs316398	0.81[JPT][hapmap]
rs316405	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs316411	0.94[JPT][hapmap]
rs33910990	0.93[ASN][1000 genomes]
rs35953019	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3733839	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs4498259	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs479996	0.87[ASN][1000 genomes]
rs4866808	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4866971	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs511340	0.82[ASN][1000 genomes]
rs541143	0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs6414900	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6451672	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6451674	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451675	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs670206	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs67913249	0.83[ASN][1000 genomes]
rs6862639	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6864955	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6870418	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6871636	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6876746	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6884303	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6894506	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7701510	0.82[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs7709181	0.94[JPT][hapmap]
rs7712046	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7723426	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7729529	0.94[JPT][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	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv830274	chr5:43095551-43226087	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	138 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7730004	ZNF131	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43156600-43191200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:43162000-43191600	Weak transcription	Fetal Brain Male	brain
3	chr5:43163800-43191800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:43164400-43191200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr5:43165000-43191200	Weak transcription	Colon Smooth Muscle	Colon
6	chr5:43175000-43191800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:43175200-43191200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr5:43175200-43191200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr5:43175200-43191200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:43175200-43191600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:43175200-43191800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr5:43175200-43192000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:43175400-43191400	Weak transcription	Fetal Brain Female	brain
14	chr5:43175400-43191400	Weak transcription	Fetal Kidney	kidney
15	chr5:43175400-43191600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr5:43175400-43191800	Weak transcription	Left Ventricle	heart
17	chr5:43175400-43191800	Weak transcription	Pancreas	Pancrea
18	chr5:43175400-43191800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr5:43175400-43192200	Weak transcription	HSMM	muscle
20	chr5:43175800-43191400	Weak transcription	Brain Germinal Matrix	brain
21	chr5:43175800-43191600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr5:43176000-43191800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr5:43176800-43192200	Weak transcription	HSMMtube	muscle
24	chr5:43177800-43191600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr5:43178000-43191600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr5:43178000-43191800	Weak transcription	Esophagus	oesophagus
27	chr5:43178000-43193200	Weak transcription	Hela-S3	cervix
28	chr5:43178200-43191200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:43178200-43191800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:43178200-43191800	Weak transcription	Fetal Muscle Leg	muscle
31	chr5:43178400-43191200	Weak transcription	Liver	Liver
32	chr5:43178400-43191800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:43178800-43191400	Weak transcription	Fetal Stomach	stomach
34	chr5:43180800-43191600	Weak transcription	Adipose Nuclei	Adipose
35	chr5:43181200-43191600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr5:43181400-43191800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr5:43181600-43191200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr5:43181800-43191800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:43183000-43191400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr5:43187000-43191800	Weak transcription	Placenta	Placenta
41	chr5:43190200-43193200	Enhancers	Fetal Heart	heart
42	chr5:43190600-43191600	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr5:43190800-43191800	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr5:43191000-43191200	Active TSS	Brain Angular Gyrus	brain
45	chr5:43191000-43191200	Enhancers	Ovary	ovary
46	chr5:43191000-43191400	Active TSS	Brain Substantia Nigra	brain
47	chr5:43191000-43191600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:43191000-43191600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:43191000-43191600	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr5:43191000-43191600	Enhancers	HepG2	liver

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