Variant report

Variant	rs3758251
Chromosome Location	chr9:100613700-100613701
allele	C/G
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	POLR2A	chr9:100613245-100613708	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr9:100613478-100614224	H1-neurons	neurons:	n/a	n/a
3	SP1	chr9:100613541-100614161	H1-hESC	embryonic stem cell:	n/a	chr9:100613926-100613940
4	SUZ12	chr9:100612750-100618219	NT2-D1	testis:	n/a	n/a

Variant related genes	Relation type
FOXE1	TF binding region

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10046805	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10113884	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10113907	0.82[AFR][1000 genomes]
rs10115216	0.89[CEU][hapmap]
rs10117642	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10119760	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10119795	0.81[CHB][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs10119853	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10120412	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10122541	0.86[AMR][1000 genomes]
rs10123699	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10512255	0.89[CEU][hapmap]
rs10739526	0.89[CEU][hapmap]
rs10759975	0.81[EUR][1000 genomes]
rs10759981	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10818124	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10818133	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10818175	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10983853	0.86[CHB][hapmap]
rs10983855	0.86[CHB][hapmap]
rs10983958	0.88[ASN][1000 genomes]
rs10983959	0.88[ASN][1000 genomes]
rs10984103	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10984253	0.90[CEU][hapmap]
rs1156850	0.81[ASN][1000 genomes]
rs12004762	0.89[CEU][hapmap]
rs12006522	0.89[CEU][hapmap]
rs12238579	0.81[CHB][hapmap]
rs12341377	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12342417	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12343182	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12347191	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12348304	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12348691	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13287360	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs13299924	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13300874	0.83[AFR][1000 genomes]
rs13302470	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1443434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1443435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1443436	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1561958	0.81[CHB][hapmap]
rs1561961	0.85[CEU][hapmap]
rs1867277	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1867278	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1867280	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1955143	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1955144	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1955145	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2120264	0.80[AMR][1000 genomes]
rs2401639	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2417575	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2417576	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3021526	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3758248	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3758249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3808893	0.89[CEU][hapmap]
rs3824495	0.89[CEU][hapmap]
rs4297160	0.86[ASN][1000 genomes]
rs4460498	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743139	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs6478437	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6478445	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6586	0.81[CHB][hapmap]
rs7027221	0.89[CEU][hapmap]
rs7031386	0.89[CEU][hapmap]
rs7033315	0.84[AFR][1000 genomes]
rs7033765	0.86[ASN][1000 genomes]
rs7034336	0.88[CEU][hapmap]
rs7036589	0.89[CEU][hapmap]
rs7037175	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7037324	0.89[CEU][hapmap]
rs7038998	0.92[CEU][hapmap]
rs7043516	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs7045138	0.86[ASN][1000 genomes]
rs72753507	0.83[AFR][1000 genomes]
rs72753509	0.82[AFR][1000 genomes]
rs7357707	0.84[AFR][1000 genomes]
rs7851552	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7851660	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7860144	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7868534	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7870540	0.81[ASN][1000 genomes]
rs7870795	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs874004	0.84[AFR][1000 genomes]
rs894673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907581	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs925487	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9299258	0.89[CEU][hapmap]
rs993501	0.80[AMR][1000 genomes];0.83[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	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv6627	chr9:100576258-100621034	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv825000	chr9:100613121-100618319	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3330300	chr9:100613506-100618154	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3758251	Hs.43687	cis	multi-tissue	Pritchard
rs3758251	C9orf156	cis	Frontal Cortex	GTEx
rs3758251	C9orf156	cis	Temporal Cortex	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100611600-100614000	Weak transcription	Pancreas	Pancrea
2	chr9:100613400-100613800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:100613400-100613800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
4	chr9:100613400-100613800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
5	chr9:100613400-100613800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:100613400-100613800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:100613400-100614000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:100613400-100614000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:100613400-100614000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
10	chr9:100613400-100614000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
11	chr9:100613400-100615400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
12	chr9:100613400-100615600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr9:100613400-100615600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
14	chr9:100613400-100615600	Bivalent Enhancer	Spleen	Spleen
15	chr9:100613400-100618800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:100613600-100613800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
17	chr9:100613600-100613800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
18	chr9:100613600-100613800	Flanking Bivalent TSS/Enh	NHEK	skin
19	chr9:100613600-100614000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr9:100613600-100614000	Bivalent/Poised TSS	HMEC	breast
21	chr9:100613600-100615000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
22	chr9:100613600-100615000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
23	chr9:100613600-100615000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
24	chr9:100613600-100615200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
25	chr9:100613600-100618000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell

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