Variant report

Variant	rs7575643
Chromosome Location	chr2:179333450-179333451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179312827..179317694-chr2:179330463..179334195,6	MCF-7	breast:
2	chr2:179314393..179320788-chr2:179330260..179334575,8	K562	blood:
3	chr2:179332606..179336122-chr2:179336235..179340321,5	K562	blood:
4	chr2:179332314..179335882-chr2:179342085..179345900,5	MCF-7	breast:
5	chr2:179314234..179317818-chr2:179329297..179333468,5	MCF-7	breast:
6	chr2:179332367..179333915-chr2:179342374..179344045,2	K562	blood:

Variant related genes	Relation type
ENSG00000204311	Chromatin interaction
ENSG00000079150	Chromatin interaction
ENSG00000238082	Chromatin interaction
ENSG00000180228	Chromatin interaction
ENSG00000116095	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10188593	1.00[CEU][hapmap]
rs10207436	1.00[JPT][hapmap]
rs10930831	1.00[JPT][hapmap]
rs12052983	1.00[JPT][hapmap]
rs12615347	0.90[ASN][1000 genomes]
rs13382684	0.83[EUR][1000 genomes]
rs13411588	0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs1559908	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]
rs16866334	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[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];0.99[ASN][1000 genomes]
rs16866342	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1863671	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967327	1.00[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
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	1.00[CEU][hapmap];0.98[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs2288322	1.00[JPT][hapmap]
rs2303536	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2303537	1.00[JPT][hapmap]
rs33998881	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3731750	0.84[JPT][hapmap]
rs3731754	1.00[JPT][hapmap]
rs3752689	0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs3769866	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4894017	0.90[JPT][hapmap]
rs4894020	0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs60488846	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6704545	0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6726043	0.83[ASN][1000 genomes]
rs6739142	0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs6753709	0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs7577862	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap]
rs7587593	0.83[ASN][1000 genomes]
rs7588593	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7589565	0.82[GIH][hapmap]
rs7589679	1.00[JPT][hapmap]
rs7598228	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7600176	0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs8179648	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[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	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7575643	ATP2C2	trans	parietal	SCAN
rs7575643	FKBP7	cis	lymphoblastoid	seeQTL
rs7575643	PRKRA	Cis_1M	lymphoblastoid	RTeQTL
rs7575643	ZNF385B	cis	parietal	SCAN
rs7575643	PLEKHA3	cis	lymphoblastoid	seeQTL

Chromatin state (count:65 , 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	chr2:179318000-179334200	Weak transcription	Fetal Kidney	kidney
13	chr2:179318000-179342800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:179321200-179342400	Weak transcription	HSMM	muscle
15	chr2:179321200-179342400	Weak transcription	HSMMtube	muscle
16	chr2:179322800-179339000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:179324600-179338200	Weak transcription	Fetal Brain Male	brain
18	chr2:179325000-179338800	Weak transcription	Left Ventricle	heart
19	chr2:179325600-179342000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:179325800-179338800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:179326200-179342000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:179326200-179342400	Weak transcription	Adipose Nuclei	Adipose
23	chr2:179326200-179342600	Weak transcription	Primary T cells from cord blood	blood
24	chr2:179327000-179342400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:179327200-179341800	Weak transcription	NHLF	lung
26	chr2:179327200-179342400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:179327400-179338200	Weak transcription	Right Ventricle	heart
28	chr2:179327400-179341800	Weak transcription	HUVEC	blood vessel
29	chr2:179327800-179338800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:179328200-179342600	Weak transcription	Fetal Thymus	thymus
31	chr2:179328200-179342600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:179328400-179335200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:179328800-179335200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:179329000-179335200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:179329000-179335200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:179329200-179334600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:179329200-179335000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:179329400-179335200	Strong transcription	Fetal Lung	lung
39	chr2:179330400-179338600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:179330400-179341800	Weak transcription	NH-A	brain
41	chr2:179330400-179342000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:179330600-179338800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:179330600-179342400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:179330800-179338200	Weak transcription	Ovary	ovary
45	chr2:179330800-179342600	Weak transcription	Colonic Mucosa	Colon
46	chr2:179331200-179342800	Weak transcription	Lung	lung
47	chr2:179331600-179334200	Strong transcription	Primary B cells from cord blood	blood
48	chr2:179331600-179334200	Strong transcription	Fetal Muscle Trunk	muscle
49	chr2:179331600-179334400	Strong transcription	Primary hematopoietic stem cells	blood
50	chr2:179331600-179334400	Strong transcription	Fetal Muscle Leg	muscle

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