Variant report

Variant	rs7616204
Chromosome Location	chr3:136444589-136444590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr3:136444515-136444621	GM12878	blood:	n/a	n/a
2	MEF2A	chr3:136444435-136444767	GM12878	blood:	n/a	chr3:136444640-136444661 chr3:136444642-136444663 chr3:136444644-136444660 chr3:136444647-136444656 chr3:136444642-136444663 chr3:136444643-136444659 chr3:136444640-136444661 chr3:136444642-136444663 chr3:136444646-136444657 chr3:136444644-136444659
3	MEF2A	chr3:136444405-136444795	GM12878	blood:	n/a	chr3:136444640-136444661 chr3:136444642-136444663 chr3:136444644-136444660 chr3:136444647-136444656 chr3:136444642-136444663 chr3:136444643-136444659 chr3:136444640-136444661 chr3:136444642-136444663 chr3:136444646-136444657 chr3:136444644-136444659

Variant related genes	Relation type
RNU6-789P	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10513014	0.92[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs1070232	0.93[JPT][hapmap]
rs10935186	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs11919030	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12107125	0.88[ASN][1000 genomes]
rs12486911	1.00[YRI][hapmap]
rs12630999	0.93[JPT][hapmap]
rs12635723	0.93[JPT][hapmap]
rs1280622	0.88[EUR][1000 genomes]
rs1280624	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1681817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1729951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2062322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs28489907	0.86[ASN][1000 genomes]
rs35874192	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3856637	0.93[JPT][hapmap]
rs4038578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4038587	0.92[CEU][hapmap]
rs4408829	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4521165	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4678433	0.93[JPT][hapmap]
rs4678437	0.93[JPT][hapmap]
rs4678438	0.93[JPT][hapmap]
rs6439649	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6439655	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6764567	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6789329	1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs6791142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6794351	0.93[JPT][hapmap]
rs6802702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6808312	0.93[JPT][hapmap]
rs7432375	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs7618518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7618871	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7621025	0.93[JPT][hapmap]
rs7637129	0.83[EUR][1000 genomes]
rs833752	0.93[JPT][hapmap]
rs900818	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs940174	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9813596	0.92[ASN][1000 genomes]
rs9825700	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9836231	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9845762	0.93[JPT][hapmap]

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	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7616204	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs7616204	PCCB	cis	multi-tissue	Pritchard
rs7616204	PCCB	cis	parietal	SCAN
rs7616204	MSL2	cis	parietal	SCAN
rs7616204	SPSB4	cis	cerebellum	SCAN
rs7616204	DBR1	cis	cerebellum	SCAN
rs7616204	PCCB	cis	cerebellum	SCAN
rs7616204	PCCB	cis	lymphoblastoid	seeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136390800-136447800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:136413400-136447200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:136413800-136447800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:136415200-136444600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:136415200-136446000	Weak transcription	Thymus	Thymus
6	chr3:136415400-136447200	Weak transcription	NHDF-Ad	bronchial
7	chr3:136415400-136447600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:136423400-136444600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:136426600-136453400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:136427800-136452400	Weak transcription	HUVEC	blood vessel
11	chr3:136428600-136444800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:136429400-136447200	Weak transcription	Osteobl	bone
13	chr3:136429600-136444600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:136431000-136454600	Weak transcription	Hela-S3	cervix
15	chr3:136432200-136447200	Weak transcription	Dnd41	blood
16	chr3:136432400-136444800	Weak transcription	Small Intestine	intestine
17	chr3:136432400-136447200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:136432400-136447600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:136432400-136468200	Weak transcription	Aorta	Aorta
20	chr3:136432600-136454000	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:136433200-136445000	Weak transcription	Lung	lung
22	chr3:136433200-136462600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:136435600-136444800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:136436600-136444600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:136436600-136444800	Weak transcription	Left Ventricle	heart
26	chr3:136437200-136447200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr3:136437200-136447400	Weak transcription	NHEK	skin
28	chr3:136438000-136458000	Weak transcription	Esophagus	oesophagus
29	chr3:136438200-136445000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:136438400-136447000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:136438800-136461200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:136439000-136444800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:136439200-136454400	Weak transcription	Fetal Stomach	stomach
34	chr3:136439400-136447400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:136440400-136447800	Weak transcription	Fetal Brain Male	brain
36	chr3:136441600-136447600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:136443400-136444800	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr3:136443600-136444600	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr3:136443600-136445400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:136443600-136445600	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr3:136443600-136445800	Enhancers	Stomach Mucosa	stomach
42	chr3:136443600-136445800	Enhancers	GM12878-XiMat	blood
43	chr3:136443600-136447200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:136443600-136448400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr3:136443600-136451400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:136443800-136452600	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr3:136444000-136444800	Enhancers	Rectal Smooth Muscle	rectum
48	chr3:136444000-136446200	Enhancers	Brain Anterior Caudate	brain
49	chr3:136444000-136446400	Enhancers	Colon Smooth Muscle	Colon
50	chr3:136444000-136446400	Enhancers	Fetal Heart	heart

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