Variant report

Variant	rs6840305
Chromosome Location	chr4:7942862-7942863
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	ESR1	chr4:7942782-7943189	ECC-1	luminal epithelium:	n/a	n/a
2	BACH1	chr4:7942802-7942916	H1-hESC	embryonic stem cell:	n/a	n/a
3	PBX3	chr4:7942750-7943434	SK-N-SH	brain:	n/a	n/a
4	NFIC	chr4:7942645-7943600	ECC-1	luminal epithelium:	n/a	n/a
5	TEAD4	chr4:7942709-7943468	ECC-1	luminal epithelium:	n/a	n/a
6	USF1	chr4:7942588-7942914	SK-N-SH	brain:	n/a	chr4:7942723-7942734
7	SP1	chr4:7942665-7943535	HCT-116	colon:	n/a	n/a
8	USF1	chr4:7942597-7942893	H1-hESC	embryonic stem cell:	n/a	chr4:7942723-7942734
9	YY1	chr4:7942810-7943261	ECC-1	luminal epithelium:	n/a	n/a
10	TEAD4	chr4:7942823-7943336	H1-hESC	embryonic stem cell:	n/a	n/a
11	USF1	chr4:7942515-7942926	H1-hESC	embryonic stem cell:	n/a	chr4:7942723-7942734
12	EP300	chr4:7942811-7943152	H1-hESC	embryonic stem cell:	n/a	n/a
13	TEAD4	chr4:7942831-7943288	MCF-7	breast:	n/a	n/a
14	MAX	chr4:7942701-7943338	MCF-7	breast:	n/a	n/a
15	NR2F2	chr4:7942670-7943387	MCF-7	breast:	n/a	n/a
16	HDAC2	chr4:7942822-7943333	MCF-7	breast:	n/a	n/a
17	USF2	chr4:7942595-7942905	Hela-S3	cervix:	n/a	chr4:7942723-7942734
18	POLR2A	chr4:7942858-7943248	H1-hESC	embryonic stem cell:	n/a	n/a
19	GATA3	chr4:7942688-7943385	MCF-7	breast:	n/a	n/a
20	MAX	chr4:7942656-7943891	A549	lung:	n/a	n/a
21	RXRA	chr4:7942772-7943441	SK-N-SH	brain:	n/a	n/a
22	MAX	chr4:7942623-7943342	ECC-1	luminal epithelium:	n/a	n/a
23	TCF12	chr4:7942546-7943394	ECC-1	luminal epithelium:	n/a	chr4:7943201-7943208
24	NFIC	chr4:7942547-7943542	ECC-1	luminal epithelium:	n/a	n/a
25	TEAD4	chr4:7942735-7943535	ECC-1	luminal epithelium:	n/a	n/a
26	SP1	chr4:7942813-7943342	H1-hESC	embryonic stem cell:	n/a	n/a
27	USF1	chr4:7942590-7942945	ECC-1	luminal epithelium:	n/a	chr4:7942723-7942734
28	EP300	chr4:7942782-7943218	MCF-7	breast:	n/a	n/a
29	USF1	chr4:7942548-7942901	A549	lung:	n/a	chr4:7942723-7942734
30	MAX	chr4:7942779-7943606	ECC-1	luminal epithelium:	n/a	n/a
31	RAD21	chr4:7942831-7943261	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr4:7942522-7943006	PANC-1	pancreas:	n/a	n/a
33	TEAD4	chr4:7942843-7943227	H1-hESC	embryonic stem cell:	n/a	n/a
34	USF2	chr4:7942596-7942903	H1-hESC	embryonic stem cell:	n/a	chr4:7942723-7942734
35	TEAD4	chr4:7942836-7943239	MCF-7	breast:	n/a	n/a
36	ZNF217	chr4:7942830-7943259	MCF-7	breast:	n/a	n/a
37	SP1	chr4:7942807-7943266	H1-hESC	embryonic stem cell:	n/a	n/a
38	GATA3	chr4:7942635-7943394	MCF-7	breast:	n/a	n/a
39	HDAC2	chr4:7942798-7943294	MCF-7	breast:	n/a	n/a
40	SIN3AK20	chr4:7942775-7943478	MCF-7	breast:	n/a	n/a
41	ESR1	chr4:7942798-7943234	ECC-1	luminal epithelium:	n/a	n/a
42	USF1	chr4:7942539-7942957	SK-N-SH_RA	brain:	n/a	chr4:7942723-7942734
43	RAD21	chr4:7942746-7943333	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr4:7942851-7943322	HCT-116	colon:	n/a	n/a
45	NR2F2	chr4:7942710-7943473	MCF-7	breast:	n/a	n/a
46	TCF12	chr4:7942716-7943492	ECC-1	luminal epithelium:	n/a	chr4:7943201-7943208
47	POLR2A	chr4:7942844-7942891	Hela-S3	cervix:	n/a	n/a
48	EP300	chr4:7942642-7943632	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
AFAP1	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12696835	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1344223	0.90[CEU][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2385912	0.81[EUR][1000 genomes]
rs2385914	0.90[CEU][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28446696	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34072960	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58349148	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60272249	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6447872	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs66479458	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846757	0.95[CEU][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7669433	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7669645	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7695142	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7695170	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7698368	0.95[CEU][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9993085	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[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	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6840305	WDR1	cis	cerebellum	SCAN
rs6840305	AFAP	cis	multi-tissue	Pritchard

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7941600-7943200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:7941600-7944000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:7941600-7944400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:7941600-7951200	Weak transcription	Small Intestine	intestine
5	chr4:7941800-7943600	Enhancers	Fetal Heart	heart
6	chr4:7942000-7943000	Weak transcription	NHLF	lung
7	chr4:7942000-7943200	Enhancers	Esophagus	oesophagus
8	chr4:7942000-7943200	Enhancers	Fetal Muscle Trunk	muscle
9	chr4:7942000-7943200	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr4:7942000-7943200	Enhancers	HSMMtube	muscle
11	chr4:7942000-7943400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr4:7942000-7943400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr4:7942000-7943400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:7942000-7943400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:7942000-7943400	Enhancers	HMEC	breast
16	chr4:7942000-7943600	Enhancers	Osteobl	bone
17	chr4:7942000-7943800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr4:7942000-7943800	Enhancers	Adipose Nuclei	Adipose
19	chr4:7942000-7943800	Enhancers	Pancreas	Pancrea
20	chr4:7942000-7943800	Enhancers	Stomach Mucosa	stomach
21	chr4:7942000-7943800	Enhancers	HepG2	liver
22	chr4:7942000-7943800	Enhancers	HSMM	muscle
23	chr4:7942000-7944000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:7942000-7944000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:7942000-7944200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:7942000-7944200	Enhancers	Fetal Intestine Large	intestine
27	chr4:7942000-7944200	Enhancers	NHDF-Ad	bronchial
28	chr4:7942000-7944400	Enhancers	Fetal Intestine Small	intestine
29	chr4:7942000-7944600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:7942000-7945200	Enhancers	A549	lung
31	chr4:7942000-7945400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:7942000-7945400	Enhancers	Placenta	Placenta
33	chr4:7942000-7945400	Enhancers	Placenta Amnion	Placenta Amnion
34	chr4:7942000-7946200	Weak transcription	Liver	Liver
35	chr4:7942000-7946400	Weak transcription	Colon Smooth Muscle	Colon
36	chr4:7942000-7946400	Weak transcription	Fetal Stomach	stomach
37	chr4:7942000-7950400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:7942000-7951000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr4:7942000-7951400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr4:7942200-7943000	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr4:7942200-7943200	Enhancers	HUVEC	blood vessel
42	chr4:7942200-7943400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:7942200-7943400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr4:7942200-7943600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:7942200-7943800	Enhancers	H9 Cell Line	embryonic stem cell
46	chr4:7942200-7944000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr4:7942200-7944000	Enhancers	NHEK	skin
48	chr4:7942200-7944800	Weak transcription	Fetal Muscle Leg	muscle
49	chr4:7942200-7947400	Weak transcription	Fetal Brain Male	brain
50	chr4:7942200-7950600	Weak transcription	Stomach Smooth Muscle	stomach

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