Variant report

Variant	rs1840680
Chromosome Location	chr3:157156029-157156030
allele	A/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	E2F6	chr3:157155118-157156183	A549	lung:	n/a	chr3:157156150-157156157 chr3:157155908-157155917 chr3:157156150-157156157 chr3:157155909-157155916 chr3:157156150-157156157 chr3:157155909-157155916 chr3:157155909-157155916 chr3:157155906-157155920 chr3:157155905-157155917
2	MAX	chr3:157155087-157156173	ECC-1	luminal epithelium:	n/a	n/a
3	RCOR1	chr3:157154051-157156393	IMR90	lung:	n/a	n/a
4	POLR2A	chr3:157155037-157156147	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr3:157155055-157156520	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr3:157154220-157161217	HUVEC	blood vessel:	n/a	n/a
7	TCF12	chr3:157155437-157156041	ECC-1	luminal epithelium:	n/a	n/a
8	MXI1	chr3:157154085-157156888	IMR90	lung:	n/a	n/a
9	POLR2A	chr3:157155164-157156097	H1-hESC	embryonic stem cell:	n/a	n/a
10	MYC	chr3:157155344-157156135	H1-hESC	embryonic stem cell:	n/a	n/a
11	REST	chr3:157154329-157156447	H1-neurons	neurons:	n/a	chr3:157155725-157155738 chr3:157156301-157156311 chr3:157156195-157156215
12	POLR2A	chr3:157154436-157156114	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr3:157154231-157157688	HUVEC	blood vessel:	n/a	n/a
14	TAF1	chr3:157155142-157156075	H1-hESC	embryonic stem cell:	n/a	n/a
15	E2F6	chr3:157155225-157156113	K562	blood:	n/a	chr3:157155908-157155917 chr3:157155909-157155916 chr3:157155909-157155916 chr3:157155909-157155916 chr3:157155906-157155920 chr3:157155905-157155917
16	MAX	chr3:157155117-157156106	H1-hESC	embryonic stem cell:	n/a	n/a
17	HA-E2F1	chr3:157155169-157156222	MCF-7	breast:	n/a	chr3:157156150-157156157 chr3:157155908-157155917 chr3:157156150-157156157 chr3:157155909-157155916 chr3:157156150-157156157 chr3:157155909-157155916 chr3:157155909-157155916 chr3:157155906-157155920 chr3:157155905-157155917
18	POLR2A	chr3:157155409-157156252	K562	blood:	n/a	n/a
19	MAX	chr3:157155024-157156163	A549	lung:	n/a	n/a
20	TAF1	chr3:157155042-157156132	H1-neurons	neurons:	n/a	n/a
21	BRCA1	chr3:157155721-157156053	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr3:157155029-157156106	SK-N-SH	brain:	n/a	n/a
23	MAX	chr3:157155079-157156078	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr3:157154415-157156673	SK-N-SH	brain:	n/a	n/a
25	JUND	chr3:157155239-157156044	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr3:157154494-157156099	ProgFib	skin:	n/a	n/a
27	POLR2A	chr3:157155113-157156462	H1-hESC	embryonic stem cell:	n/a	n/a
28	ZNF263	chr3:157155171-157156177	HEK293-T-REx	kidney:	n/a	n/a
29	REST	chr3:157155306-157156073	HL-60	blood:	n/a	chr3:157155725-157155738
30	E2F4	chr3:157155670-157156084	MCF10A-Er-Src	breast:	n/a	chr3:157155908-157155917 chr3:157155909-157155916 chr3:157155909-157155916 chr3:157155909-157155916 chr3:157155906-157155920 chr3:157155905-157155917
31	SIN3A	chr3:157154592-157156321	H1-hESC	embryonic stem cell:	n/a	chr3:157156200-157156211
32	MAX	chr3:157155015-157156324	ECC-1	luminal epithelium:	n/a	n/a
33	CTBP2	chr3:157155169-157156375	H1-hESC	embryonic stem cell:	n/a	n/a
34	TAF1	chr3:157155134-157156245	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr3:157154238-157163149	HUVEC	blood vessel:	n/a	n/a
36	KAP1	chr3:157154431-157156253	HEK293	kidney:	n/a	n/a
37	POLR2A	chr3:157155111-157156164	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr3:157154445-157156671	H1-hESC	embryonic stem cell:	n/a	n/a
39	E2F6	chr3:157155030-157156376	H1-hESC	embryonic stem cell:	n/a	chr3:157156150-157156157 chr3:157156322-157156337 chr3:157155908-157155917 chr3:157156150-157156157 chr3:157155909-157155916 chr3:157156150-157156157 chr3:157155909-157155916 chr3:157155909-157155916 chr3:157156300-157156310 chr3:157155906-157155920 chr3:157155905-157155917
40	MYC	chr3:157154306-157156057	NB4	blood:	n/a	n/a
41	POLR2A	chr3:157154320-157156276	U87	brain:	n/a	n/a
42	E2F6	chr3:157155122-157156130	H1-hESC	embryonic stem cell:	n/a	chr3:157155908-157155917 chr3:157155909-157155916 chr3:157155909-157155916 chr3:157155909-157155916 chr3:157155906-157155920 chr3:157155905-157155917
43	POLR2A	chr3:157154326-157156405	U87	brain:	n/a	n/a
44	POLR2A	chr3:157154338-157156741	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr3:157154518-157157545	SK-N-SH	brain:	n/a	n/a
46	MAX	chr3:157155132-157156087	SK-N-SH	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:157155998-157156048	A549	lung:	n/a
2	chr3:157155998-157156048	AG10803	skin:	n/a
3	chr3:157155998-157156048	NH-A	brain:	n/a
4	chr3:157155998-157156048	HEEpiC	esophagus:	n/a
5	chr3:157155998-157156048	SK-N-SH_RA	brain:	n/a
6	chr3:157155998-157156048	MCF-7	breast:	n/a
7	chr3:157155998-157156048	HUVEC	blood vessel:	n/a
8	chr3:157155998-157156048	AoSMC	blood vessel:	n/a
9	chr3:157155998-157156048	T-47D	breast:	n/a
10	chr3:157155998-157156048	BJ	skin:	n/a
11	chr3:157155998-157156048	GM12891	blood:	n/a
12	chr3:157155998-157156048	H1-hESC	embryonic stem cell:	embryo
13	chr3:157155998-157156048	SAEC	small airway:	n/a
14	chr3:157155998-157156048	HMEC	breast:	n/a
15	chr3:157155998-157156048	CMK	blood:	n/a
16	chr3:157155998-157156048	PrEC	prostate:	n/a
17	chr3:157155998-157156048	Hepatocyte	liver:	n/a
18	chr3:157155998-157156048	ProgFib	skin:	n/a
19	chr3:157155998-157156048	Jurkat	blood:	n/a
20	chr3:157155998-157156048	K562	blood:	n/a
21	chr3:157155998-157156048	ECC-1	luminal epithelium:	n/a
22	chr3:157155998-157156048	GM12892	blood:	n/a
23	chr3:157155998-157156048	HRPEpiC	eye:	n/a
24	chr3:157155998-157156048	HPAEpiC	pulmonary alveolar:	n/a
25	chr3:157155998-157156048	HepG2	liver:	n/a
26	chr3:157155998-157156048	U87	brain:	n/a
27	chr3:157155998-157156048	AG04449	skin:	fetal
28	chr3:157155998-157156048	AG09309	skin:	n/a
29	chr3:157155998-157156048	HAEpiC	amniotic membrane:	n/a
30	chr3:157155998-157156048	SKMC	muscle:	n/a
31	chr3:157155998-157156048	NB4	blood:	n/a
32	chr3:157155998-157156048	ovcar-3	ovarian:	n/a
33	chr3:157155998-157156048	HCM	heart:	n/a
34	chr3:157155998-157156048	HEK293	kidney:	embryo
35	chr3:157155998-157156048	AG09319	gingival:	n/a
36	chr3:157155998-157156048	HL-60	blood:	n/a
37	chr3:157155998-157156048	NHDF-neo	bronchial:	n/a
38	chr3:157155998-157156048	HCF	heart:	n/a
39	chr3:157155998-157156048	HNPCEpiC	eye:	n/a
40	chr3:157155998-157156048	HRCEpiC	kidney:	n/a
41	chr3:157155998-157156048	SK-N-MC	brain:	n/a
42	chr3:157155998-157156048	Hela-S3	cervix:	n/a
43	chr3:157155998-157156048	HIPEpiC	eye:	n/a
44	chr3:157155998-157156048	GM12878	blood:	n/a
45	chr3:157155998-157156048	NT2-D1	testis:	n/a
46	chr3:157155998-157156048	HCPEpiC	choroid plexus:	n/a
47	chr3:157155998-157156048	LNCaP	prostate:	n/a
48	chr3:157155998-157156048	PANC-1	pancreas:	n/a
49	chr3:157155998-157156048	PFSK-1	brain:	n/a
50	chr3:157155998-157156048	SK-N-SH	brain:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:157150749..157153721-chr3:157154855..157157411,2	K562	blood:

Variant related genes	Relation type
VEPH1	TF binding region
VEPH1	CpG island

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10936090	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1869857	0.80[JPT][hapmap]
rs2120243	0.82[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305619	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2316706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2316708	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2316709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2316710	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28638274	0.80[JPT][hapmap]
rs2873258	0.81[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3816527	0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4680364	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4680367	0.88[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6803043	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6803236	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7609926	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7616177	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7626884	0.95[YRI][hapmap]
rs7634847	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7648322	0.80[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289982	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9681270	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9868133	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1840680	PEX6	trans	cerebellum	SCAN
rs1840680	PTX3	cis	cerebellum	SCAN
rs1840680	BRD7	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157154000-157158000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:157154200-157156200	Active TSS	Brain Germinal Matrix	brain
3	chr3:157154200-157156400	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr3:157154200-157156400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr3:157154200-157156400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:157154200-157156400	Active TSS	Fetal Lung	lung
7	chr3:157154200-157156600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:157154200-157156600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:157154200-157157200	Active TSS	HSMM	muscle
10	chr3:157154200-157157400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr3:157154200-157157800	Active TSS	HSMMtube	muscle
12	chr3:157154400-157156200	Active TSS	Fetal Brain Female	brain
13	chr3:157154400-157156400	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr3:157154400-157156400	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr3:157154400-157156600	Active TSS	Fetal Kidney	kidney
16	chr3:157154400-157157000	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr3:157154600-157156200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:157154600-157156200	Active TSS	HUVEC	blood vessel
19	chr3:157154600-157156400	Active TSS	Fetal Heart	heart
20	chr3:157154600-157156400	Active TSS	Left Ventricle	heart
21	chr3:157154600-157156600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:157154600-157156600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:157154600-157156600	Active TSS	Colon Smooth Muscle	Colon
24	chr3:157154600-157156600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr3:157154600-157156600	Active TSS	Psoas Muscle	Psoas
26	chr3:157154600-157156800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:157154600-157156800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
28	chr3:157154600-157157200	Active TSS	Rectal Smooth Muscle	rectum
29	chr3:157154600-157160800	Transcr. at gene 5' and 3'	Osteobl	bone
30	chr3:157154600-157161000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:157154800-157156200	Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr3:157154800-157156200	Active TSS	Aorta	Aorta
33	chr3:157154800-157156400	Active TSS	Right Atrium	heart
34	chr3:157154800-157156800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
35	chr3:157155000-157156200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:157155000-157156200	Flanking Active TSS	Right Ventricle	heart
37	chr3:157155000-157156200	Flanking Active TSS	HMEC	breast
38	chr3:157155000-157156400	Active TSS	Ovary	ovary
39	chr3:157155000-157156400	Bivalent Enhancer	Stomach Mucosa	stomach
40	chr3:157155000-157156600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
41	chr3:157155000-157156600	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr3:157155000-157156600	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr3:157155000-157159400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:157155200-157156200	Active TSS	Brain Angular Gyrus	brain
45	chr3:157155200-157156200	Bivalent/Poised TSS	Thymus	Thymus
46	chr3:157155200-157156400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:157155200-157156400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:157155200-157156400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
49	chr3:157155200-157156400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
50	chr3:157155200-157156400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

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