Variant report

Variant	rs10786240
Chromosome Location	chr10:97666538-97666539
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	MAFK	chr10:97666448-97666985	HepG2	liver:	n/a	chr10:97666621-97666637 chr10:97666621-97666636
2	MAFK	chr10:97666463-97668125	Hela-S3	cervix:	n/a	chr10:97666621-97666637 chr10:97666621-97666636
3	MAFK	chr10:97666459-97666950	IMR90	lung:	n/a	chr10:97666621-97666637 chr10:97666621-97666636
4	MAFK	chr10:97666463-97666808	HepG2	liver:	n/a	chr10:97666621-97666637 chr10:97666621-97666636
5	USF2	chr10:97666486-97666610	HepG2	liver:	n/a	n/a
6	MAFK	chr10:97666465-97667039	K562	blood:	n/a	chr10:97666621-97666637 chr10:97666621-97666636
7	CTCF	chr10:97666440-97666590	HPAF	blood vessel:	n/a	n/a
8	MXI1	chr10:97666417-97668422	SK-N-SH	brain:	n/a	n/a
9	MAFF	chr10:97666460-97666832	HepG2	liver:	n/a	chr10:97666619-97666637
10	HCFC1	chr10:97666521-97668575	Hela-S3	cervix:	n/a	n/a
11	MAFF	chr10:97666459-97667009	K562	blood:	n/a	chr10:97666619-97666637

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97664446..97666704-chr10:97842579..97844240,2	K562	blood:
2	chr10:97665969..97667709-chr10:97802060..97805145,4	MCF-7	breast:

Variant related genes	Relation type
C10orf131	TF binding region
ENSG00000226688	Chromatin interaction
ENSG00000107443	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10786241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786242	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10786245	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10786250	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs10882684	0.84[AFR][1000 genomes]
rs10882686	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882690	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11188497	0.80[JPT][hapmap]
rs11188513	0.95[GIH][hapmap]
rs11188517	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11188518	0.88[JPT][hapmap]
rs1137629	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12244559	0.82[CHB][hapmap]
rs2027200	0.82[CHB][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap]
rs2153914	0.95[GIH][hapmap]
rs3181129	0.82[CHB][hapmap]
rs4254003	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4303172	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4415682	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4614366	0.82[CHB][hapmap]
rs7101331	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7904410	0.82[CHB][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap]
rs7906654	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7908420	0.82[CHB][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap]
rs7908691	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7921331	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs7922217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7922992	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv895905	chr10:97513362-97686064	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv895906	chr10:97513362-97703650	Weak transcription Enhancers Strong 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	10 gene(s)	inside rSNPs	diseases
4	nsv895907	chr10:97529318-97686064	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats 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 target site	10 gene(s)	inside rSNPs	diseases
5	nsv895908	chr10:97544513-97724247	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10786240	CYP2C19	cis	parietal	SCAN
rs10786240	ENTPD1	cis	multi-tissue	Pritchard
rs10786240	TCTN3	cis	lymphoblastoid	seeQTL
rs10786240	PDE6C	cis	cerebellum	SCAN
rs10786240	ENTPD1	cis	Lymphoblastoid	GTEx
rs10786240	ALDH18A1	cis	cerebellum	SCAN
rs10786240	ENTPD1	cis	lymphoblastoid	seeQTL
rs10786240	ZNF518A	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97621000-97666800	Weak transcription	Gastric	stomach
2	chr10:97622800-97666600	Weak transcription	Thymus	Thymus
3	chr10:97623800-97666600	Weak transcription	Right Ventricle	heart
4	chr10:97628000-97666800	Weak transcription	Esophagus	oesophagus
5	chr10:97632200-97667000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr10:97633400-97666600	Weak transcription	Brain Angular Gyrus	brain
7	chr10:97633800-97666600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr10:97633800-97666600	Weak transcription	Brain Hippocampus Middle	brain
9	chr10:97634400-97666800	Weak transcription	Lung	lung
10	chr10:97634600-97666800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr10:97634800-97667000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr10:97635800-97666600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr10:97638600-97666600	Weak transcription	Colonic Mucosa	Colon
14	chr10:97643200-97666600	Weak transcription	Fetal Heart	heart
15	chr10:97649400-97666600	Weak transcription	Fetal Intestine Large	intestine
16	chr10:97650000-97666600	Weak transcription	Fetal Intestine Small	intestine
17	chr10:97653800-97666600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr10:97655200-97666600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr10:97655800-97666600	Weak transcription	HSMMtube	muscle
20	chr10:97656400-97666800	Weak transcription	Psoas Muscle	Psoas
21	chr10:97656600-97666600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr10:97658000-97666600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr10:97659200-97666600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr10:97660200-97666800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr10:97660600-97666600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr10:97660600-97666800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr10:97660600-97666800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr10:97661600-97666600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr10:97662000-97666600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr10:97663200-97666600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr10:97663200-97666600	Weak transcription	Colon Smooth Muscle	Colon
32	chr10:97663600-97666600	Weak transcription	Primary B cells from cord blood	blood
33	chr10:97663600-97666600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr10:97663600-97666600	Weak transcription	Brain Substantia Nigra	brain
35	chr10:97663600-97666600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr10:97663600-97666800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr10:97663600-97667000	Weak transcription	Spleen	Spleen
38	chr10:97663800-97666800	Weak transcription	Ovary	ovary
39	chr10:97663800-97666800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr10:97664200-97666600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr10:97664200-97666600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr10:97664200-97666800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr10:97664200-97666800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr10:97664200-97666800	Weak transcription	Left Ventricle	heart
45	chr10:97664400-97666800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr10:97664600-97666800	Weak transcription	Placenta	Placenta
47	chr10:97664800-97666600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr10:97664800-97666600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr10:97665200-97666600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr10:97666400-97666600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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