Variant report

Variant	rs6753709
Chromosome Location	chr2:179319391-179319392
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179313693..179317837-chr2:179319182..179322709,8	K562	blood:
2	chr2:179319205..179322423-chr2:179341743..179345832,4	K562	blood:
3	chr2:179314981..179317756-chr2:179318011..179323890,9	K562	blood:

Variant related genes	Relation type
ENSG00000079150	Chromatin interaction
ENSG00000180228	Chromatin interaction
ENSG00000116095	Chromatin interaction
ENSG00000204311	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1001238	0.82[CHB][hapmap]
rs10207436	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs10930831	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12052983	0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13382684	0.81[EUR][1000 genomes]
rs13411588	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[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1559908	1.00[JPT][hapmap]
rs1560221	0.82[CHB][hapmap]
rs16866334	1.00[JPT][hapmap]
rs16866342	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16866400	0.82[CHB][hapmap]
rs16866420	0.82[CHB][hapmap]
rs1967327	0.95[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1978580	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2016615	0.91[ASN][1000 genomes]
rs2042996	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2059691	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2114582	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]
rs2163009	0.82[CHB][hapmap]
rs2249737	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2288320	0.90[GIH][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs2288322	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2303536	1.00[JPT][hapmap]
rs2303537	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2366603	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2366751	0.82[CHB][hapmap]
rs2886712	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3731750	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs3731754	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3752689	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3769866	0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs3813250	0.86[CHB][hapmap]
rs3829746	0.82[CHB][hapmap]
rs4894017	0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4894018	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4894019	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4894020	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]
rs4894029	0.82[CHB][hapmap]
rs6704545	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6710856	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6726043	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6739142	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[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6758838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7575643	0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs7577862	1.00[JPT][hapmap]
rs7587593	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7589679	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs7598228	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7600176	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7602597	0.86[CEU][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs8179648	0.95[JPT][hapmap]
rs9288019	0.84[ASW][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[YRI][hapmap]
rs957875	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs967507	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9808377	0.82[CHB][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	esv1817469	chr2:179296271-179319391	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6753709	PRKRA	cis	lymphoblastoid	seeQTL
rs6753709	PRKRA	cis	cerebellum	SCAN
rs6753709	PRKRA	Cis_1M	lymphoblastoid	RTeQTL
rs6753709	FKBP7	cis	parietal	SCAN
rs6753709	FKBP7	cis	lymphoblastoid	seeQTL
rs6753709	PLEKHA3	cis	lymphoblastoid	seeQTL
rs6753709	ATP2C2	trans	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179316800-179319400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:179316800-179319600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:179316800-179319600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:179316800-179320200	Weak transcription	HSMMtube	muscle
5	chr2:179316800-179320400	Weak transcription	NH-A	brain
6	chr2:179316800-179320600	Weak transcription	HSMM	muscle
7	chr2:179316800-179322000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:179316800-179327800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:179316800-179329000	Weak transcription	Liver	Liver
10	chr2:179316800-179329400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:179316800-179329800	Weak transcription	Ovary	ovary
12	chr2:179316800-179338200	Weak transcription	Fetal Stomach	stomach
13	chr2:179316800-179338800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:179316800-179341800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:179316800-179342400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:179316800-179342600	Weak transcription	Aorta	Aorta
17	chr2:179316800-179342800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:179317000-179329000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:179317000-179342000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:179317200-179328800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:179317200-179329200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:179317200-179329200	Weak transcription	Dnd41	blood
23	chr2:179317200-179342800	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:179317400-179341200	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:179317400-179341600	Weak transcription	GM12878-XiMat	blood
26	chr2:179317800-179329200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:179317800-179329200	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:179317800-179338200	Weak transcription	Osteobl	bone
29	chr2:179318000-179319800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:179318000-179322600	Weak transcription	Fetal Lung	lung
31	chr2:179318000-179329200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:179318000-179332400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:179318000-179334200	Weak transcription	Fetal Kidney	kidney
34	chr2:179318000-179342800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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