Variant report

Variant	rs6425233
Chromosome Location	chr1:173394054-173394055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173392621..173394893-chr1:173446400..173448143,2	MCF-7	breast:
2	chr1:173384577..173387294-chr1:173392404..173396188,3	MCF-7	breast:
3	chr1:173391693..173394474-chr1:173452509..173454513,2	K562	blood:
4	chr1:173392536..173394729-chr1:173398389..173400168,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117592	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10753081	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10798282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10912617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10912618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12092383	0.81[CHB][hapmap]
rs12140760	1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs4255417	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4276950	1.00[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];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4325171	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4382766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916220	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916355	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916358	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4916359	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916361	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4916362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4916363	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55654074	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425231	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6696012	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6702835	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7314	0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap]
rs7537938	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]
rs7540065	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.84[ASN][1000 genomes]
rs7556003	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9425718	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9425719	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9425723	0.84[ASN][1000 genomes]
rs9425724	0.84[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6425233	TNFSF18	cis	parietal	SCAN
rs6425233	GPR52	cis	parietal	SCAN
rs6425233	TNFSF4	cis	parietal	SCAN
rs6425233	PRDX6	cis	parietal	SCAN
rs6425233	DARS2	cis	cerebellum	SCAN
rs6425233	PRDX6	cis	cerebellum	SCAN
rs6425233	FASLG	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173372000-173398600	Weak transcription	Brain Substantia Nigra	brain
2	chr1:173375200-173398600	Weak transcription	Esophagus	oesophagus
3	chr1:173376200-173429000	Weak transcription	Gastric	stomach
4	chr1:173376400-173400800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:173378400-173398400	Weak transcription	Brain Angular Gyrus	brain
6	chr1:173379000-173398400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:173380200-173398400	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:173380200-173398600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:173380200-173398600	Weak transcription	Psoas Muscle	Psoas
10	chr1:173380400-173398400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:173380400-173398600	Weak transcription	Thymus	Thymus
12	chr1:173380400-173398800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:173383000-173398600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:173385600-173398600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:173385600-173398600	Weak transcription	Spleen	Spleen
16	chr1:173386000-173397800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr1:173387600-173429000	Weak transcription	Lung	lung
18	chr1:173387800-173398400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:173387800-173398600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:173388000-173398400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:173388000-173398400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:173388000-173398600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:173389600-173394200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:173389600-173394200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:173389600-173394200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:173389600-173394400	Weak transcription	A549	lung
27	chr1:173389600-173394600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:173389600-173395200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:173389600-173395400	Weak transcription	Colonic Mucosa	Colon
30	chr1:173389600-173398000	Weak transcription	Fetal Stomach	stomach
31	chr1:173389600-173398000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:173389600-173398400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:173389600-173398400	Weak transcription	Primary B cells from cord blood	blood
34	chr1:173389600-173398400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:173389600-173398400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:173389600-173398400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr1:173389600-173398400	Weak transcription	NH-A	brain
38	chr1:173389600-173398600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:173389600-173398600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:173389600-173398600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:173389600-173398600	Weak transcription	Left Ventricle	heart
42	chr1:173389600-173399200	Weak transcription	Pancreas	Pancrea
43	chr1:173389600-173400600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:173389800-173398000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr1:173389800-173398400	Weak transcription	Fetal Lung	lung
46	chr1:173390000-173394200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:173390000-173397800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:173390000-173398200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:173390000-173398400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:173390000-173398400	Weak transcription	Primary T helper cells PMA-I stimulated	--

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