Variant report

Variant	rs17102768
Chromosome Location	chr14:35284284-35284285
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10136352	0.81[JPT][hapmap]
rs10150083	0.80[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs11847610	0.90[ASN][1000 genomes]
rs1200414	0.81[JPT][hapmap]
rs12431818	1.00[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];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12432567	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12433706	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs12435778	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12435859	0.85[EUR][1000 genomes]
rs12586459	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12586462	1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12587021	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12587251	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12587390	0.87[CHB][hapmap];0.99[ASN][1000 genomes]
rs12587913	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12588318	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12590112	0.90[JPT][hapmap]
rs12590268	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13379337	0.82[CHB][hapmap]
rs1400745	0.90[JPT][hapmap]
rs17102726	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17102795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17102829	0.82[CEU][hapmap];0.90[JPT][hapmap]
rs17526787	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs1959154	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2295468	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2383675	0.90[ASN][1000 genomes]
rs2383676	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2383677	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs34072166	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34245772	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3783315	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3783316	0.81[JPT][hapmap]
rs5016735	0.90[ASN][1000 genomes]
rs55979964	0.92[ASN][1000 genomes]
rs58268256	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58587072	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59678582	0.85[EUR][1000 genomes]
rs61981198	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61981200	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61981202	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61981204	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61981228	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61981232	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61981234	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61981236	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61981237	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61988010	0.94[ASN][1000 genomes]
rs61988011	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61988012	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61988013	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61988044	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61988045	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7142012	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7148400	0.81[JPT][hapmap]
rs7150069	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7153289	0.95[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs7155348	0.89[ASN][1000 genomes]
rs8005470	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8005659	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[MEX][hapmap];0.85[EUR][1000 genomes]
rs8010504	0.89[ASN][1000 genomes]
rs8010579	0.87[CHB][hapmap]
rs8016548	0.84[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	esv3392700	chr14:34989406-35365530	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv1041857	chr14:35084889-35417180	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1052162	chr14:35245349-35451187	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1053722	chr14:35257458-35465784	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17102768	SNX6	cis	parietal	SCAN
rs17102768	SCFD1	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35231200-35291800	Weak transcription	Fetal Brain Male	brain
2	chr14:35232600-35293200	Weak transcription	Fetal Kidney	kidney
3	chr14:35234200-35311600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr14:35252200-35301000	Weak transcription	Psoas Muscle	Psoas
5	chr14:35265000-35296000	Weak transcription	Colon Smooth Muscle	Colon
6	chr14:35267800-35292200	Weak transcription	Right Ventricle	heart
7	chr14:35269200-35298000	Weak transcription	Ovary	ovary
8	chr14:35269400-35322200	Weak transcription	Fetal Brain Female	brain
9	chr14:35269400-35341600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr14:35269800-35290000	Weak transcription	Placenta	Placenta
11	chr14:35270200-35286800	Weak transcription	Fetal Heart	heart
12	chr14:35270400-35303400	Weak transcription	Stomach Mucosa	stomach
13	chr14:35271800-35291400	Weak transcription	Spleen	Spleen
14	chr14:35271800-35326400	Weak transcription	Esophagus	oesophagus
15	chr14:35272000-35290000	Weak transcription	Small Intestine	intestine
16	chr14:35272000-35296200	Weak transcription	Brain Germinal Matrix	brain
17	chr14:35272200-35291200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr14:35272400-35290800	Weak transcription	Fetal Stomach	stomach
19	chr14:35272400-35300200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr14:35272400-35333600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr14:35274200-35311800	Weak transcription	HSMMtube	muscle
22	chr14:35274400-35296400	Weak transcription	Aorta	Aorta
23	chr14:35274400-35303400	Weak transcription	Left Ventricle	heart
24	chr14:35274400-35312400	Weak transcription	Gastric	stomach
25	chr14:35274600-35293000	Weak transcription	Fetal Lung	lung
26	chr14:35274800-35290800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr14:35274800-35312400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr14:35275000-35288800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr14:35275200-35298000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr14:35276200-35307200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr14:35276200-35342400	Weak transcription	Pancreas	Pancrea
32	chr14:35276400-35291200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr14:35276400-35291600	Weak transcription	Thymus	Thymus
34	chr14:35276400-35297800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr14:35276400-35329600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr14:35276400-35330000	Weak transcription	Colonic Mucosa	Colon
37	chr14:35276600-35291200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr14:35276600-35320000	Weak transcription	Fetal Muscle Leg	muscle
39	chr14:35276800-35286800	Weak transcription	Hela-S3	cervix
40	chr14:35276800-35288400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr14:35276800-35288400	Weak transcription	HMEC	breast
42	chr14:35276800-35288800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr14:35276800-35293000	Weak transcription	NHLF	lung
44	chr14:35276800-35293600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr14:35276800-35293600	Weak transcription	K562	blood
46	chr14:35277000-35288600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr14:35277000-35288600	Weak transcription	Osteobl	bone
48	chr14:35277000-35289600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr14:35277000-35289800	Weak transcription	Primary B cells from cord blood	blood
50	chr14:35277000-35300600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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