Variant report

Variant	rs6704545
Chromosome Location	chr2:179341953-179341954
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:179341919-179342074	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr2:179341626-179344256	SK-N-SH	brain:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:179277322..179281063-chr2:179341771..179345640,5	K562	blood:
2	chr2:179312045..179317660-chr2:179337933..179347437,24	MCF-7	breast:
3	chr2:179319205..179322423-chr2:179341743..179345832,4	K562	blood:
4	chr2:179310863..179318324-chr2:179338966..179346608,29	K562	blood:
5	chr2:179341858..179343792-chr2:179500377..179502025,2	K562	blood:
6	chr2:179314444..179318442-chr2:179340876..179346721,19	MCF-7	breast:
7	chr2:179311363..179318324-chr2:179340414..179346232,28	K562	blood:
8	chr2:178127221..178129853-chr2:179341742..179345099,3	K562	blood:

No data

Variant related genes	Relation type
PLEKHA3	TF binding region
ENSG00000180228	Chromatin interaction
ENSG00000222043	Chromatin interaction
ENSG00000223960	Chromatin interaction
ENSG00000204311	Chromatin interaction
ENSG00000237298	Chromatin interaction
ENSG00000116044	Chromatin interaction
ENSG00000238082	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1001238	0.86[CHB][hapmap]
rs10207436	0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10930831	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12052983	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[ASN][1000 genomes]
rs13411588	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];0.80[EUR][1000 genomes]
rs1559908	0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1560221	0.86[CHB][hapmap]
rs16866334	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs16866342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16866400	0.86[CHB][hapmap]
rs16866420	0.86[CHB][hapmap]
rs1863671	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1967327	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs1978580	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2016615	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2042996	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2059691	0.85[JPT][hapmap]
rs2114582	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs2163009	0.86[CHB][hapmap]
rs2249737	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2288320	0.93[GIH][hapmap];0.85[TSI][hapmap]
rs2288322	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2303536	1.00[JPT][hapmap]
rs2303537	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs2366751	0.86[CHB][hapmap]
rs2886712	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33998881	0.81[ASN][1000 genomes]
rs3731750	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs3731754	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3752689	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3769864	0.81[CHB][hapmap]
rs3769866	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3813250	0.81[CHB][hapmap]
rs3829746	0.86[CHB][hapmap]
rs4894017	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs4894018	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4894019	0.80[EUR][1000 genomes]
rs4894020	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]
rs4894029	0.86[CHB][hapmap]
rs60488846	0.81[ASN][1000 genomes]
rs6710856	0.89[AMR][1000 genomes];0.95[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];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739142	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6753709	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]
rs6758838	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7575643	0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7577862	1.00[JPT][hapmap]
rs7587593	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588593	0.81[ASN][1000 genomes]
rs7589679	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7598228	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]
rs7600176	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7602597	1.00[ASW][hapmap];0.86[CEU][hapmap];0.83[TSI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8179648	0.95[JPT][hapmap]
rs9288019	0.81[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs957875	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs967507	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9808377	0.86[CHB][hapmap]
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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6704545	ATP2C2	trans	parietal	SCAN
rs6704545	PRKRA	cis	cerebellum	SCAN
rs6704545	PRKRA	Cis_1M	lymphoblastoid	RTeQTL
rs6704545	FKBP7	cis	lymphoblastoid	seeQTL
rs6704545	PLEKHA3	cis	lymphoblastoid	seeQTL
rs6704545	PRKRA	cis	lymphoblastoid	seeQTL
rs6704545	PLEKHA3	cis	Lymphoblastoid	GTEx
rs6704545	FKBP7	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179316800-179342400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr2:179316800-179342600	Weak transcription	Aorta	Aorta
3	chr2:179316800-179342800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:179317000-179342000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:179317200-179342800	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:179318000-179342800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:179321200-179342400	Weak transcription	HSMM	muscle
8	chr2:179321200-179342400	Weak transcription	HSMMtube	muscle
9	chr2:179325600-179342000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:179326200-179342000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:179326200-179342400	Weak transcription	Adipose Nuclei	Adipose
12	chr2:179326200-179342600	Weak transcription	Primary T cells from cord blood	blood
13	chr2:179327000-179342400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:179327200-179342400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:179328200-179342600	Weak transcription	Fetal Thymus	thymus
16	chr2:179328200-179342600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:179330400-179342000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:179330600-179342400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr2:179330800-179342600	Weak transcription	Colonic Mucosa	Colon
20	chr2:179331200-179342800	Weak transcription	Lung	lung
21	chr2:179331600-179342400	Weak transcription	Psoas Muscle	Psoas
22	chr2:179331800-179342000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:179332800-179342600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr2:179333000-179342400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:179334200-179342400	Weak transcription	Primary B cells from cord blood	blood
26	chr2:179334200-179342400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr2:179334400-179342000	Weak transcription	Fetal Intestine Large	intestine
28	chr2:179335000-179342400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:179339000-179342600	Weak transcription	Brain Angular Gyrus	brain
30	chr2:179339000-179342600	Weak transcription	Right Ventricle	heart
31	chr2:179339200-179342400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:179339400-179342000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr2:179339400-179342000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr2:179339400-179342800	Weak transcription	Fetal Heart	heart
35	chr2:179339600-179342400	Weak transcription	Fetal Stomach	stomach
36	chr2:179339800-179342800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:179339800-179342800	Weak transcription	Left Ventricle	heart
38	chr2:179340600-179342200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:179341000-179342400	Weak transcription	Fetal Brain Male	brain
40	chr2:179341200-179342800	Flanking Active TSS	Dnd41	blood
41	chr2:179341200-179346000	Active TSS	Fetal Brain Female	brain
42	chr2:179341400-179342000	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:179341400-179343600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:179341400-179344200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:179341600-179342000	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr2:179341600-179342000	Weak transcription	Fetal Muscle Leg	muscle
47	chr2:179341600-179342200	Flanking Active TSS	K562	blood
48	chr2:179341600-179342400	Enhancers	Primary hematopoietic stem cells	blood
49	chr2:179341600-179342600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:179341600-179344200	Active TSS	Fetal Lung	lung

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