Variant report

Variant	rs4894020
Chromosome Location	chr2:179288690-179288691
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179286572..179289755-chr2:179312139..179315712,3	K562	blood:
2	chr2:179285812..179289755-chr2:179312373..179317057,5	K562	blood:
3	chr2:179287041..179288843-chr2:179316178..179317718,2	MCF-7	breast:
4	chr2:179279482..179281290-chr2:179287442..179289650,2	K562	blood:

Variant related genes	Relation type
ENSG00000204311	Chromatin interaction
ENSG00000180228	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10179153	0.96[ASN][1000 genomes]
rs10188593	0.85[EUR][1000 genomes]
rs10207436	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs10930831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12052983	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs13411588	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1559908	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs16866334	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs16866342	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1967327	0.91[GIH][hapmap];0.89[TSI][hapmap]
rs1978580	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs2042996	0.84[JPT][hapmap]
rs2059691	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2114582	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs2249737	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2288320	0.95[GIH][hapmap];0.89[TSI][hapmap]
rs2288322	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs2303536	1.00[JPT][hapmap]
rs2303537	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2366603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366604	0.95[ASN][1000 genomes]
rs28773318	0.84[EUR][1000 genomes]
rs2886712	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3731750	0.84[JPT][hapmap]
rs3731754	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3752689	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3769866	0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs3769867	0.84[EUR][1000 genomes]
rs3813250	0.82[CHB][hapmap]
rs4894017	0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4894018	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894019	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57115861	0.84[EUR][1000 genomes]
rs6704545	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs6710856	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6739142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6753709	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6758838	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7575643	0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs7577862	1.00[JPT][hapmap]
rs7589679	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7598228	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7600176	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7602597	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs8179648	0.95[JPT][hapmap]
rs9288019	0.84[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs957875	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs967507	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs9967820	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv979349	chr2:179279539-179296355	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4894020	PRKRA	Cis_1M	lymphoblastoid	RTeQTL
rs4894020	PLEKHA3	cis	Lymphoblastoid	GTEx
rs4894020	FKBP7	cis	lymphoblastoid	seeQTL
rs4894020	PLEKHA3	cis	lymphoblastoid	seeQTL
rs4894020	PRKRA	cis	lymphoblastoid	seeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179278800-179291200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:179278800-179292800	Weak transcription	Spleen	Spleen
3	chr2:179278800-179293200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:179278800-179298800	Weak transcription	Small Intestine	intestine
5	chr2:179279400-179291200	Weak transcription	Lung	lung
6	chr2:179279600-179291200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:179279600-179295000	Weak transcription	Right Ventricle	heart
8	chr2:179279600-179298800	Weak transcription	Colonic Mucosa	Colon
9	chr2:179279800-179291000	Weak transcription	Thymus	Thymus
10	chr2:179279800-179291200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:179279800-179291200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:179279800-179291200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:179279800-179291200	Weak transcription	Left Ventricle	heart
14	chr2:179279800-179291200	Weak transcription	Ovary	ovary
15	chr2:179279800-179293800	Weak transcription	Placenta	Placenta
16	chr2:179279800-179295400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:179279800-179299200	Weak transcription	Esophagus	oesophagus
18	chr2:179279800-179313800	Weak transcription	Stomach Mucosa	stomach
19	chr2:179280000-179289200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:179280000-179290000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:179280000-179290400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:179280000-179291200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:179280000-179291200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:179280000-179291200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:179280000-179291200	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:179280000-179291200	Weak transcription	Fetal Thymus	thymus
27	chr2:179280000-179291200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:179280000-179291200	Weak transcription	NH-A	brain
29	chr2:179280000-179291400	Weak transcription	A549	lung
30	chr2:179280000-179291600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:179280000-179292600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:179280000-179293600	Weak transcription	Liver	Liver
33	chr2:179280000-179293800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:179280000-179294000	Weak transcription	Brain Substantia Nigra	brain
35	chr2:179280000-179296800	Weak transcription	NHLF	lung
36	chr2:179280000-179297600	Weak transcription	Hela-S3	cervix
37	chr2:179280000-179298400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:179280000-179305200	Weak transcription	Fetal Brain Male	brain
39	chr2:179280000-179310600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:179280200-179289400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:179280200-179290000	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:179280200-179291200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:179280200-179291200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:179280200-179291200	Weak transcription	Fetal Stomach	stomach
45	chr2:179280200-179291200	Weak transcription	K562	blood
46	chr2:179280200-179291400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr2:179280200-179293800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr2:179280200-179293800	Weak transcription	HUVEC	blood vessel
49	chr2:179280200-179296600	Weak transcription	Fetal Kidney	kidney
50	chr2:179280200-179314600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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