Variant report

Variant	rs7598228
Chromosome Location	chr2:179339606-179339607
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179332606..179336122-chr2:179336235..179340321,5	K562	blood:
2	chr2:179312045..179317660-chr2:179337933..179347437,24	MCF-7	breast:
3	chr2:179319284..179320885-chr2:179339018..179341944,2	MCF-7	breast:
4	chr2:179310863..179318324-chr2:179338966..179346608,29	K562	blood:
5	chr2:179315309..179317085-chr2:179338029..179339680,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238082	Chromatin interaction
ENSG00000180228	Chromatin interaction
ENSG00000204311	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10207436	1.00[JPT][hapmap]
rs10930831	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12052983	1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[ASN][1000 genomes]
rs13411588	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1559908	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16866334	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs16866342	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1863671	0.83[ASN][1000 genomes]
rs1978580	1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2016615	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2042996	0.83[JPT][hapmap]
rs2059691	0.84[JPT][hapmap]
rs2114582	0.94[JPT][hapmap]
rs2249737	0.84[JPT][hapmap]
rs2288322	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2303536	1.00[JPT][hapmap]
rs2303537	1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[ASN][1000 genomes]
rs2886712	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33998881	0.81[ASN][1000 genomes]
rs3731750	0.83[JPT][hapmap]
rs3731754	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3752689	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3769866	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4894017	1.00[JPT][hapmap]
rs4894018	1.00[CEU][hapmap]
rs4894020	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs60488846	0.81[ASN][1000 genomes]
rs6704545	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710856	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6723399	0.82[ASN][1000 genomes]
rs6726043	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739142	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6753709	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6758838	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7575643	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7577862	1.00[JPT][hapmap]
rs7587593	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588593	0.81[ASN][1000 genomes]
rs7589679	1.00[JPT][hapmap]
rs7600176	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7602597	0.86[CEU][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8179648	0.94[JPT][hapmap]
rs9288019	1.00[JPT][hapmap]
rs967507	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9967820	1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7598228	PRKRA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179316800-179341800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:179316800-179342400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr2:179316800-179342600	Weak transcription	Aorta	Aorta
4	chr2:179316800-179342800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:179317000-179342000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:179317200-179342800	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:179317400-179341200	Weak transcription	Colon Smooth Muscle	Colon
8	chr2:179317400-179341600	Weak transcription	GM12878-XiMat	blood
9	chr2:179318000-179342800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:179321200-179342400	Weak transcription	HSMM	muscle
11	chr2:179321200-179342400	Weak transcription	HSMMtube	muscle
12	chr2:179325600-179342000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:179326200-179342000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:179326200-179342400	Weak transcription	Adipose Nuclei	Adipose
15	chr2:179326200-179342600	Weak transcription	Primary T cells from cord blood	blood
16	chr2:179327000-179342400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:179327200-179341800	Weak transcription	NHLF	lung
18	chr2:179327200-179342400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr2:179327400-179341800	Weak transcription	HUVEC	blood vessel
20	chr2:179328200-179342600	Weak transcription	Fetal Thymus	thymus
21	chr2:179328200-179342600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:179330400-179341800	Weak transcription	NH-A	brain
23	chr2:179330400-179342000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:179330600-179342400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:179330800-179342600	Weak transcription	Colonic Mucosa	Colon
26	chr2:179331200-179342800	Weak transcription	Lung	lung
27	chr2:179331600-179342400	Weak transcription	Psoas Muscle	Psoas
28	chr2:179331800-179342000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:179332200-179341800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:179332800-179342600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr2:179333000-179342400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:179333400-179341800	Weak transcription	Fetal Intestine Small	intestine
33	chr2:179334200-179342400	Weak transcription	Primary B cells from cord blood	blood
34	chr2:179334200-179342400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr2:179334400-179341600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:179334400-179342000	Weak transcription	Fetal Intestine Large	intestine
37	chr2:179334600-179340600	Weak transcription	Dnd41	blood
38	chr2:179334600-179341800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:179334600-179341800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:179335000-179342400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:179335200-179340400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:179335200-179341600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:179335200-179341600	Weak transcription	Fetal Lung	lung
44	chr2:179338000-179339800	Enhancers	Fetal Brain Female	brain
45	chr2:179338200-179339800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:179338800-179339800	Enhancers	Left Ventricle	heart
47	chr2:179339000-179341400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:179339000-179342600	Weak transcription	Brain Angular Gyrus	brain
49	chr2:179339000-179342600	Weak transcription	Right Ventricle	heart
50	chr2:179339200-179340600	Weak transcription	Brain Germinal Matrix	brain

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