Variant report

Variant	rs10417820
Chromosome Location	chr19:52726346-52726347
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52697956..52699548-chr19:52724688..52727509,2	K562	blood:
2	chr19:52725400..52727782-chr19:52737067..52738597,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1025279	1.00[JPT][hapmap]
rs10402209	1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10402638	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10403154	0.94[ASW][hapmap];0.91[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10403202	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10403806	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10404236	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10404437	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407502	1.00[JPT][hapmap]
rs10407987	1.00[JPT][hapmap]
rs10408119	1.00[JPT][hapmap]
rs10412196	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10413435	1.00[JPT][hapmap];0.84[TSI][hapmap]
rs10414083	1.00[JPT][hapmap]
rs10414197	1.00[JPT][hapmap]
rs10414852	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417253	1.00[JPT][hapmap]
rs10418666	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10419304	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10420207	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs10420254	0.91[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10420560	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10420874	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421440	0.98[ASN][1000 genomes]
rs10422483	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10422838	1.00[JPT][hapmap]
rs10423610	1.00[JPT][hapmap]
rs10423794	1.00[JPT][hapmap]
rs10424348	1.00[JPT][hapmap]
rs10425135	0.94[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10426066	1.00[JPT][hapmap]
rs10426786	0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs1056348	0.88[ASW][hapmap];0.91[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11879419	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13344984	1.00[JPT][hapmap]
rs16983548	1.00[JPT][hapmap]
rs16983549	1.00[JPT][hapmap]
rs16983557	1.00[JPT][hapmap]
rs16983598	0.94[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16983601	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16983603	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs17835942	0.84[TSI][hapmap]
rs2016457	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2288409	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288410	0.91[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2303685	0.88[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560871	1.00[JPT][hapmap]
rs3745097	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4458121	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509628	0.95[CHD][hapmap]
rs7252174	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254030	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254774	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256125	0.89[CHD][hapmap]
rs7256300	0.89[CHD][hapmap]
rs7256312	0.89[CHD][hapmap]
rs7256719	0.89[CHD][hapmap]
rs7259175	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73935052	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs755531	0.88[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8100048	1.00[JPT][hapmap]
rs8100500	0.82[CHB][hapmap];1.00[CHD][hapmap];0.98[ASN][1000 genomes]
rs8100600	0.82[CHB][hapmap];0.95[CHD][hapmap];0.84[TSI][hapmap];0.95[ASN][1000 genomes]
rs8101990	1.00[JPT][hapmap];0.84[TSI][hapmap]
rs8103874	1.00[JPT][hapmap]
rs8105432	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8105792	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8106271	0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.90[ASN][1000 genomes]
rs8106544	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs8107377	1.00[JPT][hapmap]
rs8108636	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8109061	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8109512	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8110857	0.90[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8110881	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10417820	SLC27A5	cis	parietal	SCAN
rs10417820	RPL28	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52694600-52732800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:52695400-52732200	Strong transcription	Fetal Lung	lung
3	chr19:52695400-52733200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr19:52696000-52732200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr19:52696000-52732400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:52696000-52733000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:52696200-52729200	Strong transcription	Fetal Intestine Large	intestine
8	chr19:52696200-52732400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr19:52696200-52732400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr19:52696200-52732400	Strong transcription	Primary B cells from cord blood	blood
11	chr19:52697600-52732400	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr19:52697600-52733200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:52697800-52732200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:52697800-52732400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr19:52697800-52732400	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr19:52697800-52732600	Strong transcription	Primary T cells from cord blood	blood
17	chr19:52697800-52733000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:52698000-52730400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:52698000-52732200	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr19:52698000-52732200	Strong transcription	Dnd41	blood
21	chr19:52698200-52732000	Strong transcription	GM12878-XiMat	blood
22	chr19:52698200-52732400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr19:52698200-52732400	Strong transcription	HepG2	liver
24	chr19:52698200-52732600	Strong transcription	Fetal Brain Female	brain
25	chr19:52698400-52732400	Strong transcription	Fetal Thymus	thymus
26	chr19:52698600-52732000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr19:52698800-52732400	Strong transcription	Liver	Liver
28	chr19:52700800-52732200	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr19:52702200-52731800	Strong transcription	Primary B cells from peripheral blood	blood
30	chr19:52702200-52732200	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr19:52702600-52732200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr19:52703000-52731600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr19:52703000-52732600	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr19:52703000-52734600	Strong transcription	Fetal Stomach	stomach
35	chr19:52703200-52731200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr19:52703200-52732200	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:52703200-52732400	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr19:52703200-52732400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr19:52703200-52732800	Strong transcription	Brain Germinal Matrix	brain
40	chr19:52703200-52733200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr19:52703200-52734000	Strong transcription	Lung	lung
42	chr19:52703400-52726400	Strong transcription	Fetal Intestine Small	intestine
43	chr19:52703600-52733200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr19:52703800-52732200	Strong transcription	NHEK	skin
45	chr19:52703800-52733200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr19:52704000-52732200	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr19:52704000-52732400	Strong transcription	Brain Cingulate Gyrus	brain
48	chr19:52704000-52733200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr19:52704200-52731400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:52704200-52731800	Strong transcription	HUVEC	blood vessel

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