Variant report

Variant	rs17670897
Chromosome Location	chr5:74097552-74097553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10062244	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1043968	1.00[JPT][hapmap]
rs10515189	0.90[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs10515191	1.00[JPT][hapmap]
rs11556477	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739122	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11740871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11741464	0.81[ASN][1000 genomes]
rs11741789	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11742773	0.83[ASN][1000 genomes]
rs11743655	0.83[JPT][hapmap]
rs11746069	0.90[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap]
rs11746611	0.89[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs11746702	0.85[JPT][hapmap]
rs11747965	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11749137	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11948188	1.00[JPT][hapmap]
rs11955898	1.00[JPT][hapmap]
rs1350097	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1447453	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1531103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs15694	0.85[JPT][hapmap]
rs16872299	0.85[JPT][hapmap]
rs16872333	0.80[ASN][1000 genomes]
rs16872346	1.00[JPT][hapmap]
rs16872347	0.80[ASN][1000 genomes]
rs16872364	0.80[ASN][1000 genomes]
rs16878945	0.82[LWK][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes]
rs17670701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17670867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17670975	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17671140	0.89[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17738111	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]
rs17738266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17738565	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17738645	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17738674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17852781	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1812122	0.84[ASN][1000 genomes]
rs1992712	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1993370	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1993372	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2044410	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2061162	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2084116	0.83[ASN][1000 genomes]
rs2084118	0.83[ASN][1000 genomes]
rs2084119	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2100033	0.83[ASN][1000 genomes]
rs3733794	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3932895	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3968877	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4594835	0.80[ASN][1000 genomes]
rs56068548	0.80[ASN][1000 genomes]
rs56202905	0.80[ASN][1000 genomes]
rs58184895	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61093699	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62366366	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62366371	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62366373	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62366375	0.81[ASN][1000 genomes]
rs62366376	0.81[ASN][1000 genomes]
rs62366406	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62366413	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62366414	0.83[ASN][1000 genomes]
rs62366415	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62366416	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62366418	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62366419	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62366420	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62366421	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62366423	0.80[ASN][1000 genomes]
rs62366424	0.80[ASN][1000 genomes]
rs62366426	0.80[ASN][1000 genomes]
rs62366450	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62366453	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62366454	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62366455	0.80[ASN][1000 genomes]
rs62366456	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62366457	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62366458	0.80[ASN][1000 genomes]
rs62366459	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62367765	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62367766	0.80[ASN][1000 genomes]
rs62367767	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6453077	0.85[JPT][hapmap]
rs6453084	1.00[JPT][hapmap]
rs6453086	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6453087	1.00[JPT][hapmap]
rs6859014	0.85[JPT][hapmap]
rs6866082	1.00[JPT][hapmap]
rs6873067	0.80[ASN][1000 genomes]
rs6874094	0.83[ASN][1000 genomes]
rs6874609	1.00[JPT][hapmap]
rs6877116	1.00[JPT][hapmap]
rs6877442	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6879781	1.00[JPT][hapmap]
rs6882499	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6883061	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6884843	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6885093	0.85[JPT][hapmap]
rs6885675	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6890815	0.83[ASN][1000 genomes]
rs6897698	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6897904	0.80[ASN][1000 genomes]
rs72764640	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72764681	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7708203	0.92[JPT][hapmap]
rs7717223	0.80[ASN][1000 genomes]
rs7724292	0.80[ASN][1000 genomes]
rs7728889	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs820828	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs820830	0.90[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs820834	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9686657	1.00[JPT][hapmap];0.83[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17670897	GFM2	cis	parietal	SCAN
rs17670897	NSA2	cis	cerebellum	SCAN
rs17670897	NSA2	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74064000-74112400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:74064200-74102000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:74064400-74134600	Weak transcription	Fetal Brain Male	brain
4	chr5:74064800-74101200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:74066600-74112800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr5:74069000-74153000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:74069600-74102600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr5:74070000-74111600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr5:74074200-74102600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr5:74074800-74102200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr5:74074800-74143400	Weak transcription	Primary B cells from cord blood	blood
12	chr5:74081200-74101200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:74081200-74101200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr5:74081400-74097800	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr5:74081400-74101400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr5:74081600-74098000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr5:74081600-74098600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:74081800-74101200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:74082400-74097800	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr5:74083200-74098000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:74085800-74098000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:74087600-74112000	Weak transcription	A549	lung
23	chr5:74087600-74130000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr5:74088800-74101200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:74090800-74099200	Strong transcription	HepG2	liver
26	chr5:74091000-74097800	Strong transcription	Dnd41	blood
27	chr5:74091400-74098200	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr5:74095800-74097600	Weak transcription	HMEC	breast
29	chr5:74095800-74097800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:74095800-74146000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr5:74096000-74097600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr5:74096000-74097600	Weak transcription	Fetal Intestine Small	intestine
33	chr5:74096000-74097600	Weak transcription	Fetal Stomach	stomach
34	chr5:74096000-74097600	Weak transcription	Spleen	Spleen
35	chr5:74096000-74097600	Weak transcription	NHLF	lung
36	chr5:74096000-74097800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr5:74096000-74100000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr5:74096000-74100400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr5:74096000-74100600	Weak transcription	Brain Anterior Caudate	brain
40	chr5:74096000-74102400	Weak transcription	Ovary	ovary
41	chr5:74096000-74103000	Weak transcription	Thymus	Thymus
42	chr5:74096000-74106600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:74096000-74112400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr5:74096000-74113400	Weak transcription	Brain Angular Gyrus	brain
45	chr5:74096000-74131000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:74096000-74134200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr5:74096000-74134200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr5:74096000-74137200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr5:74096000-74137200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr5:74096200-74098400	Weak transcription	Brain Substantia Nigra	brain

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