Variant report

Variant	rs322825
Chromosome Location	chr7:127721507-127721508
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	POLR2A	chr7:127721372-127722526	K562	blood:	n/a	n/a
2	POLR2A	chr7:127721458-127721670	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:127721407-127721615	K562	blood:	n/a	n/a
4	POLR2A	chr7:127721340-127721822	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:127712887..127715958-chr7:127718524..127721736,3	K562	blood:

Variant related genes	Relation type
MIR593	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1024910	0.90[AMR][1000 genomes]
rs11768841	0.82[AMR][1000 genomes]
rs1193331	0.82[AMR][1000 genomes]
rs1193333	0.86[AMR][1000 genomes]
rs1193335	0.88[AMR][1000 genomes]
rs124756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241291	0.82[ASW][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs2543477	0.83[AMR][1000 genomes]
rs322776	0.83[AFR][1000 genomes]
rs322781	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs322813	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs322816	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322817	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs322819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322820	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322821	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322822	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs322823	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322824	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs322826	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs322827	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs322828	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs322829	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs322830	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs322832	0.97[ASN][1000 genomes]
rs322833	0.97[ASN][1000 genomes]
rs322837	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs322840	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3757753	0.98[ASN][1000 genomes]
rs3757754	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3757759	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3757760	0.82[ASW][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs3757763	0.85[CHB][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes]
rs3757771	0.84[AMR][1000 genomes]
rs3779522	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3779523	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3779527	0.91[AMR][1000 genomes]
rs3808055	0.98[ASN][1000 genomes]
rs3808056	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap]
rs3808078	0.80[AMR][1000 genomes]
rs3808086	0.82[AMR][1000 genomes]
rs3808088	0.81[CHB][hapmap];0.91[MEX][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes]
rs62481450	0.80[AMR][1000 genomes]
rs6467155	0.91[AMR][1000 genomes]
rs6467156	0.91[AMR][1000 genomes]
rs6969233	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7789322	0.90[AMR][1000 genomes]
rs9791922	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs322825	GPR37	cis	cerebellum	SCAN
rs322825	TCN2	trans	lymphoblastoid	seeQTL
rs322825	CCDC136	cis	parietal	SCAN
rs322825	GCC1	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127669400-127726600	Weak transcription	Hela-S3	cervix
2	chr7:127692800-127724200	Weak transcription	Right Atrium	heart
3	chr7:127701600-127724600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr7:127702800-127727800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:127707800-127742200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr7:127709800-127724600	Weak transcription	NHDF-Ad	bronchial
7	chr7:127710600-127737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:127711400-127724000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr7:127711600-127727400	Strong transcription	HepG2	liver
10	chr7:127711600-127735600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr7:127711600-127736400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr7:127711800-127721800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr7:127711800-127737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:127712000-127728800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:127712200-127738200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr7:127713000-127735000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr7:127713000-127737200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr7:127713200-127729600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr7:127713200-127736400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:127713400-127736400	Strong transcription	NHEK	skin
21	chr7:127713800-127738800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr7:127714000-127722600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr7:127714400-127721600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:127714400-127722200	Strong transcription	Placenta	Placenta
25	chr7:127714400-127722400	Strong transcription	Thymus	Thymus
26	chr7:127714400-127735000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr7:127714400-127738000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr7:127714600-127722200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr7:127714800-127734400	Strong transcription	Dnd41	blood
30	chr7:127715200-127721600	Weak transcription	Left Ventricle	heart
31	chr7:127715800-127738400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr7:127716400-127722000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr7:127716400-127722400	Strong transcription	Osteobl	bone
34	chr7:127716600-127721800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:127716800-127724800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr7:127717000-127722200	Strong transcription	Primary T cells from cord blood	blood
37	chr7:127717000-127729000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr7:127717000-127738000	Weak transcription	Fetal Kidney	kidney
39	chr7:127717200-127724000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:127717200-127725200	Weak transcription	Fetal Brain Female	brain
41	chr7:127717200-127734000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr7:127717200-127736600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr7:127717200-127738600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr7:127717400-127722600	Strong transcription	Esophagus	oesophagus
45	chr7:127717600-127721600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr7:127717600-127729600	Strong transcription	Lung	lung
47	chr7:127717600-127736600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr7:127717600-127738800	Strong transcription	Liver	Liver
49	chr7:127717800-127721800	Strong transcription	Fetal Stomach	stomach
50	chr7:127717800-127722000	Strong transcription	HSMM	muscle

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