Variant report

Variant	rs1559908
Chromosome Location	chr2:179336347-179336348
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179318518..179321253-chr2:179336311..179338289,2	K562	blood:
2	chr2:179332606..179336122-chr2:179336235..179340321,5	K562	blood:
3	chr2:179318518..179321253-chr2:179336311..179338324,4	K562	blood:
4	chr2:179314620..179317852-chr2:179335197..179337913,3	K562	blood:
5	chr2:179336273..179338307-chr2:179397796..179400668,2	K562	blood:

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

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10207436	1.00[JPT][hapmap]
rs10930831	1.00[JPT][hapmap]
rs12052983	1.00[JPT][hapmap]
rs12615347	0.90[ASN][1000 genomes]
rs13411588	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs16866334	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16866342	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs16866352	0.80[CEU][hapmap]
rs1863671	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967327	0.81[GIH][hapmap];0.85[TSI][hapmap]
rs1978580	1.00[JPT][hapmap]
rs2016615	0.80[ASN][1000 genomes]
rs2042996	0.84[JPT][hapmap]
rs2059691	0.85[JPT][hapmap]
rs2114582	0.95[JPT][hapmap]
rs2249737	0.85[JPT][hapmap]
rs2288320	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs2288322	1.00[JPT][hapmap]
rs2303536	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs2303537	1.00[JPT][hapmap]
rs33998881	0.98[ASN][1000 genomes]
rs3731750	0.84[JPT][hapmap]
rs3731754	1.00[JPT][hapmap]
rs3752689	1.00[JPT][hapmap]
rs3769866	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4894017	0.90[JPT][hapmap]
rs4894020	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs60488846	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6704545	0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6726043	0.83[ASN][1000 genomes]
rs6739142	1.00[JPT][hapmap]
rs6753709	1.00[JPT][hapmap]
rs7575643	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7577862	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs7587593	0.83[ASN][1000 genomes]
rs7588593	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7589679	1.00[JPT][hapmap]
rs7598228	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7600176	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs8179648	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs9288019	1.00[JPT][hapmap]
rs957875	0.84[JPT][hapmap]
rs967507	1.00[JPT][hapmap]
rs9967820	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1559908	PLEKHA3	cis	lymphoblastoid	seeQTL
rs1559908	ATP5G3	cis	cerebellum	SCAN
rs1559908	FKBP7	cis	lymphoblastoid	seeQTL
rs1559908	ZNF385B	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179316800-179338200	Weak transcription	Fetal Stomach	stomach
2	chr2:179316800-179338800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:179316800-179341800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:179316800-179342400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:179316800-179342600	Weak transcription	Aorta	Aorta
6	chr2:179316800-179342800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:179317000-179342000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:179317200-179342800	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:179317400-179341200	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:179317400-179341600	Weak transcription	GM12878-XiMat	blood
11	chr2:179317800-179338200	Weak transcription	Osteobl	bone
12	chr2:179318000-179342800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:179321200-179342400	Weak transcription	HSMM	muscle
14	chr2:179321200-179342400	Weak transcription	HSMMtube	muscle
15	chr2:179322800-179339000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr2:179324600-179338200	Weak transcription	Fetal Brain Male	brain
17	chr2:179325000-179338800	Weak transcription	Left Ventricle	heart
18	chr2:179325600-179342000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:179325800-179338800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr2:179326200-179342000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:179326200-179342400	Weak transcription	Adipose Nuclei	Adipose
22	chr2:179326200-179342600	Weak transcription	Primary T cells from cord blood	blood
23	chr2:179327000-179342400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:179327200-179341800	Weak transcription	NHLF	lung
25	chr2:179327200-179342400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:179327400-179338200	Weak transcription	Right Ventricle	heart
27	chr2:179327400-179341800	Weak transcription	HUVEC	blood vessel
28	chr2:179327800-179338800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:179328200-179342600	Weak transcription	Fetal Thymus	thymus
30	chr2:179328200-179342600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:179330400-179338600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:179330400-179341800	Weak transcription	NH-A	brain
33	chr2:179330400-179342000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:179330600-179338800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:179330600-179342400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:179330800-179338200	Weak transcription	Ovary	ovary
37	chr2:179330800-179342600	Weak transcription	Colonic Mucosa	Colon
38	chr2:179331200-179342800	Weak transcription	Lung	lung
39	chr2:179331600-179342400	Weak transcription	Psoas Muscle	Psoas
40	chr2:179331800-179342000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:179332200-179341800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:179332800-179342600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr2:179333000-179342400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:179333400-179341800	Weak transcription	Fetal Intestine Small	intestine
45	chr2:179334200-179338000	Weak transcription	Fetal Brain Female	brain
46	chr2:179334200-179338200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:179334200-179338600	Weak transcription	Brain Germinal Matrix	brain
48	chr2:179334200-179342400	Weak transcription	Primary B cells from cord blood	blood
49	chr2:179334200-179342400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr2:179334400-179338600	Weak transcription	Fetal Muscle Leg	muscle

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