Variant report

Variant	rs1048167
Chromosome Location	chr5:74017499-74017500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:73980026..73982895-chr5:74017239..74018833,2	K562	blood:
2	chr5:74011922..74013768-chr5:74017287..74019347,3	K562	blood:
3	chr5:74015011..74017827-chr5:74019863..74023018,4	K562	blood:
4	chr5:74011922..74013768-chr5:74017287..74019015,2	K562	blood:

Variant related genes	Relation type
ENSG00000049860	Chromatin interaction
ENSG00000207336	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10515192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10515194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10515199	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11739122	0.85[MKK][hapmap]
rs11959570	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16872220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16872231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16872235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16872242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16872259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16872323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16872345	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16872349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16872362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17561738	0.80[ASN][1000 genomes]
rs3733794	0.85[MKK][hapmap]
rs55899032	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55920995	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56127814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56192858	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56203772	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57202395	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57549677	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58864890	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60492282	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6453076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6453079	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6453082	0.95[EUR][1000 genomes]
rs6861935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6870806	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6873912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6873998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6877188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6881400	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6882035	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6883061	0.85[MKK][hapmap]
rs6883278	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6883420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6884338	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6884843	0.88[MKK][hapmap]
rs6894177	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6898684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72764630	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72764643	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72764647	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72764648	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72764650	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72764654	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72764655	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72764656	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72764657	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72764663	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72764669	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72764675	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72764676	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72764683	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72764684	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72764687	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72764690	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72766504	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7705519	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.81[EUR][1000 genomes]
rs7713812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7732440	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7732843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs957680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9686657	0.91[MKK][hapmap]
rs9765469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[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	nsv598653	chr5:73992881-74095542	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs1048167	NSA2	cis	Esophagus Mucosa	GTEx
rs1048167	TINP1	cis	multi-tissue	Pritchard
rs1048167	ZBED3	cis	parietal	SCAN
rs1048167	TINP1	cis	lesional skin	skin_eQTL
rs1048167	NSA2	cis	lymphoblastoid	seeQTL
rs1048167	NSA2	cis	parietal	SCAN
rs1048167	NSA2	cis	Artery Aorta	GTEx
rs1048167	NSA2	cis	Muscle Skeletal	GTEx
rs1048167	NSA2	cis	Nerve Tibial	GTEx
rs1048167	NSA2	cis	Heart Left Ventricle	GTEx
rs1048167	TINP1	cis	normal skin	skin_eQTL
rs1048167	NSA2	cis	cerebellum	SCAN
rs1048167	NSA2	cis	Artery Tibial	GTEx
rs1048167	NSA2	cis	Whole Blood	GTEx
rs1048167	GFM2	cis	parietal	SCAN
rs1048167	NSA2	cis	Stomach	GTEx
rs1048167	WDR41	cis	parietal	SCAN
rs1048167	NSA2	cis	Esophagus Muscularis	GTEx
rs1048167	NSA2	cis	Adipose Subcutaneous	GTEx
rs1048167	TINP1	cis	uninvolved skin	skin_eQTL
rs1048167	NSA2	cis	lung	GTEx
rs1048167	NSA2	cis	Skin Sun Exposed Lower leg	GTEx
rs1048167	NSA2	cis	Thyroid	GTEx
rs1048167	GFM2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:73982000-74061800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:73982200-74020600	Weak transcription	Fetal Brain Male	brain
3	chr5:73983000-74027000	Weak transcription	Fetal Heart	heart
4	chr5:73983200-74030200	Weak transcription	Small Intestine	intestine
5	chr5:73988400-74021000	Weak transcription	Right Ventricle	heart
6	chr5:73993800-74019800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:73999800-74017600	Weak transcription	Aorta	Aorta
8	chr5:73999800-74060800	Weak transcription	Pancreas	Pancrea
9	chr5:73999800-74062200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:74000000-74017600	Weak transcription	Psoas Muscle	Psoas
11	chr5:74002600-74019600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:74002600-74030800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:74002600-74031800	Weak transcription	Esophagus	oesophagus
14	chr5:74002600-74041200	Weak transcription	Colonic Mucosa	Colon
15	chr5:74002600-74051600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:74002600-74061800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:74008400-74028800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:74008400-74036200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:74008400-74047800	Strong transcription	Placenta	Placenta
20	chr5:74008400-74060200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr5:74008400-74060200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr5:74008600-74044200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:74008800-74035200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:74008800-74036000	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr5:74009800-74022200	Strong transcription	HMEC	breast
26	chr5:74010000-74020000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr5:74010000-74036200	Strong transcription	Liver	Liver
28	chr5:74010200-74022200	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr5:74010200-74036000	Strong transcription	Duodenum Mucosa	Duodenum
30	chr5:74010200-74038200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:74010200-74048000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:74010400-74036400	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr5:74010400-74059600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:74011200-74022200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr5:74011200-74044200	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr5:74011400-74036800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:74011800-74022400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:74012000-74022000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr5:74012000-74051600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:74012200-74050400	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr5:74012400-74018000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:74012600-74018600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:74012600-74023000	Strong transcription	Primary T cells from cord blood	blood
44	chr5:74012600-74023200	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr5:74012600-74027400	Strong transcription	Left Ventricle	heart
46	chr5:74012600-74027600	Strong transcription	Dnd41	blood
47	chr5:74012600-74034800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr5:74012800-74036200	Strong transcription	Fetal Intestine Large	intestine
49	chr5:74013000-74021600	Strong transcription	Fetal Thymus	thymus
50	chr5:74013000-74022000	Strong transcription	GM12878-XiMat	blood

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