Variant report

Variant	rs17738111
Chromosome Location	chr5:74015025-74015026
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	chr5:74013428-74015370	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74015011..74017827-chr5:74019863..74023018,4	K562	blood:

Variant related genes	Relation type
HEXB	TF binding region
ENSG00000207336	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10062244	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1043968	1.00[JPT][hapmap]
rs10515189	0.90[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10515191	1.00[JPT][hapmap]
rs11556477	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11739122	1.00[JPT][hapmap]
rs11740871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11741464	0.82[EUR][1000 genomes]
rs11741789	1.00[JPT][hapmap]
rs11743415	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11743655	0.83[JPT][hapmap]
rs11746069	0.90[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11746611	0.89[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11746702	0.85[JPT][hapmap]
rs11746717	0.82[ASN][1000 genomes]
rs11747965	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11749137	1.00[JPT][hapmap]
rs11948188	1.00[JPT][hapmap]
rs11955898	1.00[JPT][hapmap]
rs1350097	1.00[JPT][hapmap]
rs1447453	1.00[JPT][hapmap]
rs1531103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs15694	0.85[JPT][hapmap]
rs16872299	0.85[JPT][hapmap]
rs16872346	1.00[JPT][hapmap]
rs17670605	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17670701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17670867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17670897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17670975	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17671140	0.89[CEU][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17738266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17738565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17738645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17738674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17852781	0.81[ASN][1000 genomes]
rs1992712	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1993370	1.00[JPT][hapmap]
rs1993372	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2044410	1.00[JPT][hapmap]
rs2061162	1.00[JPT][hapmap]
rs2084119	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3733794	1.00[JPT][hapmap]
rs3968877	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs58184895	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61093699	0.81[ASN][1000 genomes]
rs62366366	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62366371	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62366373	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62366375	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62366376	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62366406	0.81[ASN][1000 genomes]
rs62366413	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62366415	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62366416	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62366418	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62366419	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62366420	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62366421	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62366450	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62366453	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62366454	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62366456	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62366457	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62366459	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62367765	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62367767	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6453077	0.85[JPT][hapmap]
rs6453084	1.00[JPT][hapmap]
rs6453086	1.00[JPT][hapmap]
rs6453087	1.00[JPT][hapmap]
rs6859014	0.85[JPT][hapmap]
rs6866082	1.00[JPT][hapmap]
rs6874609	1.00[JPT][hapmap]
rs6877116	1.00[JPT][hapmap]
rs6877442	1.00[JPT][hapmap]
rs6879781	1.00[JPT][hapmap]
rs6882499	1.00[JPT][hapmap]
rs6883061	1.00[JPT][hapmap]
rs6884843	1.00[JPT][hapmap]
rs6885093	0.85[JPT][hapmap]
rs6885675	1.00[JPT][hapmap]
rs6897698	1.00[JPT][hapmap]
rs72764640	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72764681	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7708203	0.92[JPT][hapmap]
rs7728889	1.00[JPT][hapmap]
rs820827	0.85[EUR][1000 genomes]
rs820828	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs820830	0.90[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs820832	0.85[EUR][1000 genomes]
rs820833	0.85[EUR][1000 genomes]
rs820834	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs820835	0.85[EUR][1000 genomes]
rs9686657	1.00[JPT][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17738111	NSA2	cis	cerebellum	SCAN
rs17738111	GFM2	cis	parietal	SCAN
rs17738111	NSA2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:73982000-74017400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:73982000-74061800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:73982200-74020600	Weak transcription	Fetal Brain Male	brain
4	chr5:73983000-74017400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:73983000-74027000	Weak transcription	Fetal Heart	heart
6	chr5:73983200-74030200	Weak transcription	Small Intestine	intestine
7	chr5:73983400-74016000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr5:73987200-74017400	Weak transcription	Fetal Kidney	kidney
9	chr5:73988400-74021000	Weak transcription	Right Ventricle	heart
10	chr5:73990000-74016200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr5:73993400-74017400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr5:73993800-74019800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:73999600-74016000	Weak transcription	Fetal Muscle Leg	muscle
14	chr5:73999800-74016000	Weak transcription	Thymus	Thymus
15	chr5:73999800-74017600	Weak transcription	Aorta	Aorta
16	chr5:73999800-74060800	Weak transcription	Pancreas	Pancrea
17	chr5:73999800-74062200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr5:74000000-74016000	Weak transcription	Lung	lung
19	chr5:74000000-74017600	Weak transcription	Psoas Muscle	Psoas
20	chr5:74000200-74016200	Weak transcription	Hela-S3	cervix
21	chr5:74002200-74016000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:74002400-74016000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr5:74002400-74016400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:74002400-74016800	Weak transcription	Brain Substantia Nigra	brain
25	chr5:74002600-74015200	Weak transcription	Fetal Intestine Small	intestine
26	chr5:74002600-74015800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr5:74002600-74015800	Weak transcription	Gastric	stomach
28	chr5:74002600-74016000	Weak transcription	Ovary	ovary
29	chr5:74002600-74016200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr5:74002600-74016200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr5:74002600-74017200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr5:74002600-74019600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:74002600-74030800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr5:74002600-74031800	Weak transcription	Esophagus	oesophagus
35	chr5:74002600-74041200	Weak transcription	Colonic Mucosa	Colon
36	chr5:74002600-74051600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:74002600-74061800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:74003400-74015800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr5:74008400-74028800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:74008400-74036200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:74008400-74047800	Strong transcription	Placenta	Placenta
42	chr5:74008400-74060200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr5:74008400-74060200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr5:74008600-74044200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:74008800-74035200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr5:74008800-74036000	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr5:74009800-74022200	Strong transcription	HMEC	breast
48	chr5:74010000-74020000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr5:74010000-74036200	Strong transcription	Liver	Liver
50	chr5:74010200-74022200	Strong transcription	Rectal Mucosa Donor 29	rectum

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