Variant report

Variant	rs7537938
Chromosome Location	chr1:173408212-173408213
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173403035..173408326-chr1:173791459..173795185,5	K562	blood:
2	chr1:173406280..173410007-chr1:173444433..173448102,3	MCF-7	breast:
3	chr1:173405237..173408410-chr1:173408631..173411366,3	K562	blood:
4	chr1:173398890..173402305-chr1:173404603..173408427,6	K562	blood:
5	chr1:173405257..173406898-chr1:173407237..173410019,2	K562	blood:
6	chr1:173407532..173410194-chr1:173412621..173414388,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117593	Chromatin interaction
ENSG00000117592	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000203739	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10753081	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10798282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10912617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10912618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10912656	0.82[CHB][hapmap]
rs12092383	0.81[CHB][hapmap]
rs12140760	1.00[CHB][hapmap];0.93[CHD][hapmap]
rs4255417	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4276950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4325171	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4382766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4916220	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4916355	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4916358	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4916359	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4916361	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4916362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4916363	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55654074	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425231	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6425233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696012	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6702835	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7314	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap]
rs7540065	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap];0.87[ASN][1000 genomes]
rs7556003	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9425718	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9425719	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9425723	0.87[ASN][1000 genomes]
rs9425724	0.87[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	nsv831915	chr1:173268424-173482157	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7537938	GPR52	cis	parietal	SCAN
rs7537938	TNFSF4	cis	parietal	SCAN
rs7537938	PRDX6	cis	parietal	SCAN
rs7537938	FASLG	cis	cerebellum	SCAN
rs7537938	PRDX6	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173376200-173429000	Weak transcription	Gastric	stomach
2	chr1:173387600-173429000	Weak transcription	Lung	lung
3	chr1:173391800-173429000	Weak transcription	Ovary	ovary
4	chr1:173399400-173408600	Weak transcription	Aorta	Aorta
5	chr1:173399400-173410000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr1:173399400-173410800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:173399400-173410800	Weak transcription	Pancreas	Pancrea
8	chr1:173399400-173414400	Weak transcription	Spleen	Spleen
9	chr1:173399400-173424200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:173399600-173408600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:173399600-173412800	Weak transcription	Thymus	Thymus
12	chr1:173399800-173413000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:173399800-173413800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:173399800-173415400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:173399800-173415600	Weak transcription	Liver	Liver
16	chr1:173400200-173421000	Weak transcription	Psoas Muscle	Psoas
17	chr1:173400200-173422800	Weak transcription	NH-A	brain
18	chr1:173400400-173429000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:173400600-173413000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:173400600-173413600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:173400600-173413800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:173400600-173428800	Weak transcription	Fetal Stomach	stomach
23	chr1:173400800-173408600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr1:173400800-173410800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr1:173400800-173410800	Weak transcription	Brain Angular Gyrus	brain
26	chr1:173400800-173411200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:173400800-173412600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:173400800-173413400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:173400800-173413800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:173400800-173413800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:173400800-173413800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:173400800-173413800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:173400800-173414000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:173400800-173414200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:173400800-173420600	Weak transcription	Hela-S3	cervix
36	chr1:173400800-173421000	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:173400800-173422800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:173400800-173429000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:173400800-173429000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:173401000-173408600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr1:173401000-173415600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:173401000-173418000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:173401000-173421000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:173401000-173421000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:173401000-173422800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:173401000-173428800	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:173401000-173429000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:173401000-173429000	Weak transcription	Left Ventricle	heart
49	chr1:173401200-173408800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr1:173401200-173410400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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