Variant report

Variant	rs4707385
Chromosome Location	chr6:88398718-88398719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88397239..88400435-chr6:88400607..88403655,3	K562	blood:
2	chr6:88384987..88388432-chr6:88394955..88398882,4	K562	blood:
3	chr6:88397124..88399437-chr6:88612572..88615497,2	K562	blood:
4	chr6:88397600..88401322-chr6:88403736..88407504,4	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1052623	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1075665	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11962148	0.95[JPT][hapmap]
rs12530371	0.94[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs13214442	0.94[JPT][hapmap]
rs2300908	0.95[JPT][hapmap]
rs3778671	0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs3818057	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4354121	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4707386	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58305152	0.86[ASN][1000 genomes]
rs6454634	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs6914244	0.83[EUR][1000 genomes]
rs6927171	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs6928057	0.95[JPT][hapmap]
rs9294384	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9294385	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444514	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs9444521	0.82[EUR][1000 genomes]
rs9444531	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9444534	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444536	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450716	0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs9450717	0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs9450740	0.85[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap]
rs9450749	0.81[ASW][hapmap];0.94[CEU][hapmap];0.80[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs9450750	0.81[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs9450751	0.93[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs9450756	0.81[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs9450760	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450763	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450773	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450775	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9474	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4707385	AKIRIN2	cis	Liver	GTEx
rs4707385	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs4707385	C6orf162	cis	parietal	SCAN
rs4707385	AK022079	cis	multi-tissue	Pritchard
rs4707385	AKIRIN2	cis	cerebellum	SCAN
rs4707385	SLC35A1	cis	parietal	SCAN
rs4707385	SLC35A1	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:88363000-88408200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:88381400-88400600	Weak transcription	Right Atrium	heart
6	chr6:88385400-88399800	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:88385400-88401200	Weak transcription	Fetal Heart	heart
8	chr6:88385800-88399200	Weak transcription	Brain Anterior Caudate	brain
9	chr6:88386200-88399000	Weak transcription	Gastric	stomach
10	chr6:88387600-88407000	Weak transcription	Fetal Kidney	kidney
11	chr6:88387800-88400600	Weak transcription	K562	blood
12	chr6:88388000-88401400	Weak transcription	Placenta	Placenta
13	chr6:88388000-88410400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:88389200-88406800	Weak transcription	Fetal Stomach	stomach
15	chr6:88389600-88401400	Weak transcription	Fetal Brain Female	brain
16	chr6:88390200-88401200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr6:88390400-88398800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:88390400-88399600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr6:88390400-88400400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:88390400-88400800	Weak transcription	Pancreas	Pancrea
21	chr6:88390400-88401200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:88390400-88401400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:88390400-88401800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:88390400-88405600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:88390400-88410000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:88391000-88405200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:88391200-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:88391400-88400800	Weak transcription	Brain Germinal Matrix	brain
29	chr6:88391400-88400800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr6:88391600-88399400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:88391800-88399600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:88392000-88399200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:88392000-88399200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:88392000-88400000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:88392000-88401200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:88392200-88400000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:88392200-88405200	Weak transcription	Fetal Brain Male	brain
38	chr6:88392400-88400600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:88392400-88400800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:88392400-88401400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr6:88392400-88407200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:88392400-88407400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:88392400-88407400	Weak transcription	Aorta	Aorta
44	chr6:88392600-88399800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:88392600-88406800	Weak transcription	HSMM	muscle
46	chr6:88392600-88407200	Weak transcription	HMEC	breast
47	chr6:88393000-88400000	Weak transcription	Osteobl	bone
48	chr6:88393000-88401200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:88393000-88401400	Weak transcription	NHEK	skin
50	chr6:88393600-88402600	Weak transcription	Esophagus	oesophagus

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