Variant report

Variant	rs4701030
Chromosome Location	chr5:178503338-178503339
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10479519	0.91[ASN][1000 genomes]
rs10479520	0.95[ASN][1000 genomes]
rs10516149	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs10516150	0.95[ASN][1000 genomes]
rs11505147	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11951738	1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs11957976	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs11958355	0.95[ASN][1000 genomes]
rs11960161	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs12152869	0.95[ASN][1000 genomes]
rs13160086	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13161528	0.95[ASN][1000 genomes]
rs13188724	0.95[ASN][1000 genomes]
rs13359549	0.84[ASN][1000 genomes]
rs13359570	0.84[ASN][1000 genomes]
rs13359572	0.82[ASN][1000 genomes]
rs13361077	0.84[ASN][1000 genomes]
rs17078988	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs17078991	1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs2047354	1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs2132671	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs2132672	0.95[ASN][1000 genomes]
rs34054398	0.95[ASN][1000 genomes]
rs34431447	0.96[ASN][1000 genomes]
rs34881171	0.95[ASN][1000 genomes]
rs35568336	0.95[ASN][1000 genomes]
rs3797615	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4700780	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700781	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4701045	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58827878	0.90[ASN][1000 genomes]
rs60061283	0.92[ASN][1000 genomes]
rs60073676	0.94[ASN][1000 genomes]
rs62393072	0.90[ASN][1000 genomes]
rs62393074	0.90[ASN][1000 genomes]
rs62393075	0.91[ASN][1000 genomes]
rs62393076	0.91[ASN][1000 genomes]
rs6601007	0.95[ASN][1000 genomes]
rs6601010	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6859576	0.90[ASN][1000 genomes]
rs6859767	0.88[ASN][1000 genomes]
rs6860309	0.95[ASN][1000 genomes]
rs6861539	0.95[ASN][1000 genomes]
rs6867119	0.88[ASN][1000 genomes]
rs6867208	0.92[ASN][1000 genomes]
rs6868893	0.88[ASN][1000 genomes]
rs6875473	0.95[ASN][1000 genomes]
rs6875622	0.95[ASN][1000 genomes]
rs6880315	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs6888539	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs6888567	0.86[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs6890317	0.91[ASN][1000 genomes]
rs6891216	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs7707587	0.95[ASN][1000 genomes]
rs7708743	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7709054	0.95[ASN][1000 genomes]
rs7711420	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs7732719	0.95[ASN][1000 genomes]
rs7733072	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1018650	chr5:178428743-178515196	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv1024994	chr5:178429975-178505167	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1025616	chr5:178429975-178515196	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS 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	6 gene(s)	inside rSNPs	diseases
8	nsv1026351	chr5:178429975-178535309	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1027487	chr5:178455495-178510587	Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv482750	chr5:178482653-178663586	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers 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	6 gene(s)	inside rSNPs	diseases
12	nsv1023392	chr5:178495775-178516483	ZNF genes & repeats Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv1021642	chr5:178495775-178535309	ZNF genes & repeats Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv1028000	chr5:178500527-178516483	ZNF genes & repeats Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv1015745	chr5:178503162-178519187	ZNF genes & repeats Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4701030	PFN3	cis	parietal	SCAN
rs4701030	TBC1D9B	cis	cerebellum	SCAN
rs4701030	SRPX	trans	multi-tissue	Pritchard
rs4701030	DKFZp686E2433	cis	Lymphoblastoid	GTEx
rs4701030	GRM6	cis	cerebellum	SCAN
rs4701030	LOC345462	cis	multi-tissue	Pritchard

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178488200-178511000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:178488400-178508400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
3	chr5:178488400-178511600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr5:178488400-178512000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:178488600-178517200	ZNF genes & repeats	Liver	Liver
6	chr5:178489400-178511400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr5:178490600-178517400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:178492200-178508400	ZNF genes & repeats	Fetal Lung	lung
9	chr5:178492600-178508000	ZNF genes & repeats	Colon Smooth Muscle	Colon
10	chr5:178492600-178512200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
11	chr5:178492600-178513400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
12	chr5:178492800-178508200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
13	chr5:178492800-178511200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:178492800-178517200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:178492800-178517200	ZNF genes & repeats	Adipose Nuclei	Adipose
16	chr5:178498400-178511000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
17	chr5:178498600-178511400	ZNF genes & repeats	Brain Germinal Matrix	brain
18	chr5:178498600-178512000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:178498600-178512000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:178499600-178508200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:178499800-178507000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:178499800-178508800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:178500000-178507200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:178500000-178507200	ZNF genes & repeats	Brain Hippocampus Middle	brain
25	chr5:178500200-178507000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
26	chr5:178500400-178507000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
27	chr5:178500400-178507200	ZNF genes & repeats	Fetal Muscle Leg	muscle
28	chr5:178500400-178508400	ZNF genes & repeats	Brain Anterior Caudate	brain
29	chr5:178500600-178506800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
30	chr5:178500600-178507000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
31	chr5:178500600-178511800	ZNF genes & repeats	Fetal Brain Female	brain
32	chr5:178500600-178512400	ZNF genes & repeats	Brain Substantia Nigra	brain
33	chr5:178500800-178505400	ZNF genes & repeats	Fetal Stomach	stomach
34	chr5:178500800-178506600	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
35	chr5:178500800-178507200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
36	chr5:178500800-178507400	ZNF genes & repeats	Fetal Brain Male	brain
37	chr5:178500800-178508200	ZNF genes & repeats	Ovary	ovary
38	chr5:178500800-178511200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
39	chr5:178501200-178507000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
40	chr5:178501200-178507000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
41	chr5:178501400-178507000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
42	chr5:178501400-178507000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
43	chr5:178501400-178507000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
44	chr5:178501400-178507000	ZNF genes & repeats	Osteobl	bone
45	chr5:178501400-178507200	ZNF genes & repeats	Fetal Heart	heart
46	chr5:178501400-178507400	ZNF genes & repeats	Brain Angular Gyrus	brain
47	chr5:178501400-178507600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
48	chr5:178501400-178508200	ZNF genes & repeats	Primary B cells from cord blood	blood
49	chr5:178501600-178507200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
50	chr5:178502200-178503400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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