Variant report

Variant	rs2675968
Chromosome Location	chr2:233736244-233736245
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:233734109-233737469	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:233735747-233737006	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr2:233735472-233738418	A549	lung:	n/a	n/a
4	MBD4	chr2:233736166-233737976	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:233735959-233739644	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:233733915-233737373	HepG2	liver:	n/a	n/a
7	CHD2	chr2:233736180-233736480	HepG2	liver:	n/a	n/a
8	NFIC	chr2:233736022-233737445	HepG2	liver:	n/a	n/a
9	MYBL2	chr2:233735996-233737757	HepG2	liver:	n/a	n/a
10	RAD21	chr2:233736128-233736430	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr2:233735463-233740850	HepG2	liver:	n/a	n/a
12	MYC	chr2:233736237-233736446	HepG2	liver:	n/a	n/a
13	MAX	chr2:233736185-233736475	HepG2	liver:	n/a	n/a
14	POLR2A	chr2:233736214-233737470	HepG2	liver:	n/a	n/a
15	YY1	chr2:233736224-233737428	HepG2	liver:	n/a	n/a
16	POLR2A	chr2:233734116-233737517	HepG2	liver:	n/a	n/a
17	HEY1	chr2:233735984-233737336	HepG2	liver:	n/a	n/a
18	TAF1	chr2:233736144-233737447	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:233730563..233732599-chr2:233735089..233737149,2	K562	blood:
2	chr2:233735745..233738389-chr2:234136756..234138303,2	MCF-7	breast:
3	chr2:233733606..233736774-chr2:233738541..233741120,3	K562	blood:
4	chr2:233733606..233736578-chr2:233738541..233742093,3	K562	blood:

No data

Variant related genes	Relation type
C2orf82	TF binding region
ENSG00000182600	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1083522	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933406	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs1104764	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs11535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12105766	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.95[YRI][hapmap]
rs12619195	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs13029336	0.83[JPT][hapmap]
rs1515961	0.83[JPT][hapmap]
rs1973675	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.95[YRI][hapmap]
rs2675953	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675954	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675972	0.94[ASN][1000 genomes]
rs283470	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs283473	0.83[JPT][hapmap]
rs4973564	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4973569	0.87[CEU][hapmap]
rs6704763	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.95[YRI][hapmap]
rs6717048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs6733495	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs709937	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs748002	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778341	0.93[ASW][hapmap];0.95[CEU][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs778370	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778371	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs938569	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs938575	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1009825	chr2:233709566-233763470	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv984452	chr2:233725452-233762965	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv999116	chr2:233733352-233759864	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1007029	chr2:233733352-233760519	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv536179	chr2:233735380-233757170	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Autism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophrenia (combined)	23453885	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2675968	TIGD1	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233722800-233738000	Weak transcription	Stomach Mucosa	stomach
2	chr2:233723000-233740400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:233723200-233736600	Weak transcription	Colonic Mucosa	Colon
4	chr2:233723200-233738600	Weak transcription	K562	blood
5	chr2:233723600-233736400	Weak transcription	Right Ventricle	heart
6	chr2:233723600-233736600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:233724200-233738600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:233724600-233738600	Weak transcription	Esophagus	oesophagus
9	chr2:233726000-233737400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:233726000-233740400	Weak transcription	HMEC	breast
11	chr2:233726200-233737400	Weak transcription	Fetal Brain Female	brain
12	chr2:233726400-233738200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:233726400-233739000	Weak transcription	Thymus	Thymus
14	chr2:233726400-233740200	Weak transcription	Primary B cells from cord blood	blood
15	chr2:233726400-233740400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:233726400-233740800	Weak transcription	HSMM	muscle
17	chr2:233726600-233737800	Weak transcription	Brain Germinal Matrix	brain
18	chr2:233726600-233738200	Weak transcription	Gastric	stomach
19	chr2:233726600-233738400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr2:233726600-233738400	Weak transcription	Placenta	Placenta
21	chr2:233726600-233738800	Weak transcription	NHLF	lung
22	chr2:233726600-233739000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:233726600-233739200	Weak transcription	Left Ventricle	heart
24	chr2:233726600-233739800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:233726600-233740000	Weak transcription	Pancreas	Pancrea
26	chr2:233726600-233740200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:233726600-233740400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:233726600-233740400	Weak transcription	Lung	lung
29	chr2:233726600-233740400	Weak transcription	NHEK	skin
30	chr2:233726800-233736400	Weak transcription	Fetal Intestine Large	intestine
31	chr2:233726800-233736600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:233726800-233755600	Weak transcription	HSMMtube	muscle
33	chr2:233727800-233738400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr2:233727800-233738600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:233729200-233736400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:233731000-233736800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr2:233732600-233738200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:233734000-233737200	Enhancers	Brain Anterior Caudate	brain
39	chr2:233734200-233736800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:233734200-233739600	Flanking Active TSS	HepG2	liver
41	chr2:233734400-233737800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr2:233734400-233740400	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr2:233734600-233740200	Enhancers	Brain Cingulate Gyrus	brain
44	chr2:233734600-233740200	Enhancers	Brain Substantia Nigra	brain
45	chr2:233734800-233740200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:233735000-233736600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:233735000-233736600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:233735000-233739200	Enhancers	Brain Angular Gyrus	brain
49	chr2:233735000-233740000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:233735000-233740000	Genic enhancers	Fetal Intestine Small	intestine

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