Variant report

Variant	rs10798282
Chromosome Location	chr1:173437024-173437025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173435562..173438278-chr1:173445966..173447922,2	MCF-7	breast:
2	chr1:173415577..173417279-chr1:173436581..173438176,2	K562	blood:

Variant related genes	Relation type
ENSG00000117592	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10753081	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10912617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10912618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10912656	0.82[CHB][hapmap]
rs12092383	0.81[CHB][hapmap]
rs12140760	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1359460	0.87[LWK][hapmap]
rs4255417	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4276950	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];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4325171	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4382766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4611	0.85[ASN][1000 genomes]
rs4916220	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4916355	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916358	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4916359	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4916362	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55654074	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6425231	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6425233	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]
rs6696012	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6702835	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7314	0.83[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7537938	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]
rs7540065	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7556003	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9425718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9425719	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9425723	0.94[ASN][1000 genomes]
rs9425724	0.81[AFR][1000 genomes];0.94[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10798282	DARS2	cis	cerebellum	SCAN
rs10798282	PRDX6	cis	cerebellum	SCAN
rs10798282	TNFSF18	cis	parietal	SCAN
rs10798282	PRDX6	cis	parietal	SCAN
rs10798282	GPR52	cis	parietal	SCAN
rs10798282	FASLG	cis	cerebellum	SCAN
rs10798282	SLC9A11	cis	parietal	SCAN
rs10798282	TNFSF4	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173419000-173439000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr1:173423800-173442400	Weak transcription	NH-A	brain
3	chr1:173425200-173442400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:173429400-173439800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:173430400-173437200	Weak transcription	NHLF	lung
6	chr1:173430400-173437800	Weak transcription	Esophagus	oesophagus
7	chr1:173430400-173439200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:173430400-173442400	Weak transcription	Gastric	stomach
9	chr1:173430400-173442800	Weak transcription	Pancreas	Pancrea
10	chr1:173430400-173444400	Weak transcription	Right Ventricle	heart
11	chr1:173430600-173438000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:173430600-173438800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:173430600-173439000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:173430600-173439800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:173430600-173442600	Weak transcription	Aorta	Aorta
16	chr1:173430600-173443200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:173430600-173444400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:173430800-173437800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:173430800-173439400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:173430800-173439800	Weak transcription	Fetal Stomach	stomach
21	chr1:173430800-173445000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:173431000-173438600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:173431000-173438800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:173431000-173439000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:173431000-173439200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:173431000-173439600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:173431000-173439600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:173431000-173439600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:173431000-173439800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:173431000-173439800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:173431000-173439800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:173431000-173442400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:173431000-173442400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:173431000-173442400	Weak transcription	Hela-S3	cervix
35	chr1:173431000-173442600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:173431000-173442600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:173431000-173444400	Weak transcription	Left Ventricle	heart
38	chr1:173431200-173439800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:173431200-173439800	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr1:173431200-173442400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr1:173431200-173442800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:173431400-173437600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:173431400-173441200	Weak transcription	HSMM	muscle
44	chr1:173431600-173442400	Weak transcription	Liver	Liver
45	chr1:173431800-173437800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr1:173432600-173439800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:173432800-173442600	Weak transcription	Fetal Heart	heart
48	chr1:173433000-173439800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:173433000-173442400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:173433200-173444200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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