Variant report

Variant	rs3764965
Chromosome Location	chr4:20714653-20714654
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10017693	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[ASN][1000 genomes]
rs10018931	1.00[ASN][1000 genomes]
rs10022322	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs10024002	0.81[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs10025286	0.87[ASN][1000 genomes]
rs10031524	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs10034054	1.00[ASN][1000 genomes]
rs10084802	0.89[YRI][hapmap]
rs10938801	0.81[CEU][hapmap];0.81[CHB][hapmap];0.93[YRI][hapmap]
rs10938803	0.88[CEU][hapmap]
rs11936560	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11940062	0.85[EUR][1000 genomes]
rs11941041	0.86[ASN][1000 genomes]
rs11944886	1.00[ASN][1000 genomes]
rs12331966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs12640448	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs12641186	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs12644782	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[ASN][1000 genomes]
rs16869886	1.00[ASN][1000 genomes]
rs16869889	0.87[ASN][1000 genomes]
rs17622371	0.82[CHB][hapmap]
rs1820505	0.85[EUR][1000 genomes]
rs1985322	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[ASN][1000 genomes]
rs2052775	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[ASN][1000 genomes]
rs2114472	1.00[ASN][1000 genomes]
rs2114473	0.97[ASN][1000 genomes]
rs2114474	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2288308	1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs2322688	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[ASN][1000 genomes]
rs28524474	0.87[ASN][1000 genomes]
rs28714128	0.82[ASN][1000 genomes]
rs28788006	0.87[ASN][1000 genomes]
rs3764964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs3764966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs3764967	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3796639	0.87[ASN][1000 genomes]
rs3815872	0.87[ASN][1000 genomes]
rs3816874	0.93[YRI][hapmap]
rs4431223	0.93[ASN][1000 genomes]
rs4510461	0.87[ASN][1000 genomes]
rs55874299	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57740160	0.82[ASN][1000 genomes]
rs59335491	0.87[ASN][1000 genomes]
rs61428210	0.81[EUR][1000 genomes]
rs62410126	0.87[ASN][1000 genomes]
rs62410129	0.83[ASN][1000 genomes]
rs62410159	0.84[ASN][1000 genomes]
rs62411662	0.80[ASN][1000 genomes]
rs6447971	0.85[EUR][1000 genomes]
rs6447972	0.85[EUR][1000 genomes]
rs6447973	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs6447974	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6447975	0.86[YRI][hapmap]
rs6447976	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[ASN][1000 genomes]
rs6447978	0.89[YRI][hapmap]
rs6447982	0.97[YRI][hapmap]
rs6811030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[ASN][1000 genomes]
rs6811505	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6811933	0.81[EUR][1000 genomes]
rs6817475	0.94[ASN][1000 genomes]
rs6831516	0.89[YRI][hapmap]
rs6857386	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs6858843	0.82[EUR][1000 genomes]
rs73240292	0.87[ASN][1000 genomes]
rs7438098	0.82[ASN][1000 genomes]
rs7655154	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs7663837	0.81[EUR][1000 genomes]
rs7666288	0.87[ASN][1000 genomes]
rs7668797	0.85[EUR][1000 genomes]
rs7673805	0.97[ASN][1000 genomes]
rs7674453	0.87[ASN][1000 genomes]
rs7681691	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs7688592	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs7689421	0.88[CEU][hapmap];0.89[YRI][hapmap]
rs7694208	0.88[CEU][hapmap];0.89[YRI][hapmap]
rs7696618	0.87[ASN][1000 genomes]
rs964019	0.83[EUR][1000 genomes]
rs990206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[ASN][1000 genomes]
rs9995697	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]

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	nsv1013077	chr4:20599841-20732558	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	esv3406683	chr4:20714554-20718752	Strong transcription Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3764965	PACRGL	cis	lung	GTEx
rs3764965	C4orf28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20702400-20722600	Weak transcription	Spleen	Spleen
2	chr4:20702600-20717200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:20703000-20717200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:20703000-20717400	Weak transcription	Fetal Heart	heart
5	chr4:20703000-20721800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:20703000-20722800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:20703000-20741400	Weak transcription	Stomach Mucosa	stomach
8	chr4:20703200-20715000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr4:20703200-20722800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:20703200-20741000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:20703400-20722800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:20703400-20722800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:20703400-20723600	Weak transcription	Pancreas	Pancrea
14	chr4:20703400-20724000	Weak transcription	A549	lung
15	chr4:20703600-20715000	Weak transcription	Ovary	ovary
16	chr4:20703600-20716200	Weak transcription	Hela-S3	cervix
17	chr4:20703600-20717200	Weak transcription	Brain Germinal Matrix	brain
18	chr4:20703800-20714800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:20705000-20718200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:20705400-20718200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:20705600-20715400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:20706000-20715200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:20706000-20715400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:20706000-20717400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:20706200-20715200	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr4:20706200-20715400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr4:20706200-20715600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:20706200-20715600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:20706600-20722600	Weak transcription	Gastric	stomach
30	chr4:20706800-20738600	Weak transcription	Psoas Muscle	Psoas
31	chr4:20707200-20714800	Weak transcription	Colon Smooth Muscle	Colon
32	chr4:20707200-20716800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:20707200-20717400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr4:20707200-20717400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:20707200-20722800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr4:20707200-20722800	Weak transcription	Thymus	Thymus
37	chr4:20707200-20723200	Weak transcription	Esophagus	oesophagus
38	chr4:20707200-20723400	Weak transcription	Colonic Mucosa	Colon
39	chr4:20707200-20724000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr4:20707200-20739400	Weak transcription	HepG2	liver
41	chr4:20707400-20717200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr4:20707400-20722600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr4:20707600-20717200	Weak transcription	Fetal Muscle Trunk	muscle
44	chr4:20707600-20717200	Weak transcription	Left Ventricle	heart
45	chr4:20707600-20717200	Weak transcription	Lung	lung
46	chr4:20707600-20717200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr4:20707600-20717400	Weak transcription	HSMMtube	muscle
48	chr4:20707600-20722200	Weak transcription	Small Intestine	intestine
49	chr4:20707600-20723000	Weak transcription	Right Ventricle	heart
50	chr4:20707600-20724000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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