Variant report

Variant	rs10410306
Chromosome Location	chr19:44601537-44601538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10406335	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs10408901	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs10413195	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10420143	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1236715	0.82[CHB][hapmap]
rs1236716	0.82[CHB][hapmap]
rs2061332	0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2061333	0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2068061	0.90[GIH][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs2168778	0.89[EUR][1000 genomes]
rs2284978	0.83[EUR][1000 genomes]
rs2284980	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes]
rs2284981	0.82[CHB][hapmap]
rs2356750	0.82[EUR][1000 genomes]
rs28446946	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28539456	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3172	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3200505	0.93[ASN][1000 genomes]
rs3746319	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs3746321	0.93[ASN][1000 genomes]
rs4239529	0.83[CHB][hapmap];0.84[EUR][1000 genomes]
rs4429390	0.83[CHB][hapmap]
rs4459653	0.83[CHB][hapmap]
rs4508518	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4802204	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4802205	0.97[ASN][1000 genomes]
rs4802206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802207	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4803676	0.83[CHB][hapmap];0.90[GIH][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs4803678	0.84[EUR][1000 genomes]
rs4803679	0.84[EUR][1000 genomes]
rs4803680	0.84[EUR][1000 genomes]
rs4803681	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs55876899	0.92[ASN][1000 genomes]
rs56353321	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62115524	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62115526	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6509141	0.83[EUR][1000 genomes]
rs7249827	0.84[EUR][1000 genomes]
rs7249834	0.84[EUR][1000 genomes]
rs7250004	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250005	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7250076	0.84[EUR][1000 genomes]
rs7250171	0.84[EUR][1000 genomes]
rs7251868	0.83[EUR][1000 genomes]
rs7508149	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7508762	0.87[EUR][1000 genomes]
rs8099869	0.82[CHB][hapmap]
rs8101657	0.84[EUR][1000 genomes]
rs8104573	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8105860	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8108021	0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs8108404	0.97[ASN][1000 genomes]
rs8113750	1.00[CEU][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9304638	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][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	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10410306	GRIN2D	cis	cerebellum	SCAN
rs10410306	SNORD34	cis	parietal	SCAN
rs10410306	ZNF223	cis	Thyroid	GTEx
rs10410306	CLPTM1	cis	cerebellum	SCAN
rs10410306	ZNF223	cis	lung	GTEx
rs10410306	TULP2	cis	cerebellum	SCAN
rs10410306	ETFB	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44599600-44601800	Weak transcription	Gastric	stomach
2	chr19:44599600-44601800	Weak transcription	Pancreas	Pancrea
3	chr19:44599600-44602600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:44599600-44604400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:44599600-44604400	Weak transcription	Spleen	Spleen
6	chr19:44599600-44604800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr19:44599600-44608000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:44599600-44609000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:44599600-44610600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr19:44599600-44611000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:44599800-44601600	Weak transcription	Fetal Kidney	kidney
12	chr19:44599800-44601800	Weak transcription	Fetal Stomach	stomach
13	chr19:44599800-44601800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr19:44599800-44601800	Weak transcription	Osteobl	bone
15	chr19:44599800-44602400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:44599800-44602600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:44599800-44604400	Weak transcription	Psoas Muscle	Psoas
18	chr19:44599800-44604600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr19:44599800-44604600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr19:44599800-44604600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr19:44599800-44604600	Weak transcription	HUVEC	blood vessel
22	chr19:44599800-44604600	Weak transcription	NH-A	brain
23	chr19:44599800-44604800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr19:44599800-44604800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr19:44599800-44605000	Weak transcription	Small Intestine	intestine
26	chr19:44599800-44605000	Weak transcription	K562	blood
27	chr19:44599800-44605200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr19:44599800-44606000	Weak transcription	Fetal Heart	heart
29	chr19:44599800-44609200	Weak transcription	NHEK	skin
30	chr19:44599800-44610400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr19:44600000-44601800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:44600000-44601800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:44600000-44601800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:44600000-44601800	Weak transcription	Esophagus	oesophagus
35	chr19:44600000-44601800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr19:44600000-44602000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:44600000-44602000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:44600000-44602600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:44600000-44602800	Weak transcription	Fetal Intestine Small	intestine
40	chr19:44600000-44603200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr19:44600000-44604000	Weak transcription	Thymus	Thymus
42	chr19:44600000-44605400	Weak transcription	NHLF	lung
43	chr19:44600000-44610400	Weak transcription	Stomach Mucosa	stomach
44	chr19:44600200-44602200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr19:44600200-44602400	Weak transcription	Brain Germinal Matrix	brain
46	chr19:44600200-44604400	Weak transcription	Right Ventricle	heart
47	chr19:44600200-44605000	Weak transcription	Colonic Mucosa	Colon
48	chr19:44600200-44605000	Weak transcription	HepG2	liver
49	chr19:44600400-44602000	Strong transcription	HSMMtube	muscle
50	chr19:44600400-44605400	Weak transcription	Hela-S3	cervix

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