Variant report

Variant	rs3807884
Chromosome Location	chr7:111845773-111845774
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	CREB1	chr7:111845317-111847490	HepG2	liver:	n/a	n/a
2	RAD21	chr7:111845303-111846879	HepG2	liver:	n/a	chr7:111845990-111846002
3	NRF1	chr7:111845464-111847542	SK-N-SH	brain:	n/a	chr7:111846495-111846504 chr7:111846080-111846089
4	SMARCC1	chr7:111845184-111847358	Hela-S3	cervix:	n/a	chr7:111846552-111846561
5	TCF7L2	chr7:111845762-111847130	HCT-116	colon:	n/a	n/a
6	RAD21	chr7:111845698-111846154	HepG2	liver:	n/a	chr7:111845990-111846002
7	TEAD4	chr7:111845403-111846786	SK-N-SH	brain:	n/a	chr7:111845633-111845642
8	CTBP2	chr7:111845133-111847412	H1-hESC	embryonic stem cell:	n/a	n/a
9	SMARCB1	chr7:111845245-111847283	Hela-S3	cervix:	n/a	chr7:111846552-111846561
10	CEBPB	chr7:111845388-111845879	IMR90	lung:	n/a	n/a
11	REST	chr7:111843971-111847587	H1-neurons	neurons:	n/a	chr7:111846001-111846011 chr7:111846491-111846504 chr7:111845994-111846012
12	TCF7L2	chr7:111845211-111847344	Hela-S3	cervix:	n/a	chr7:111845244-111845254
13	PBX3	chr7:111845693-111846908	SK-N-SH	brain:	n/a	n/a
14	RAD21	chr7:111845280-111847526	IMR90	lung:	n/a	chr7:111845990-111846002
15	HCFC1	chr7:111845609-111847418	K562	blood:	n/a	n/a
16	E2F6	chr7:111845737-111846827	K562	blood:	n/a	chr7:111846495-111846504 chr7:111846722-111846731
17	YY1	chr7:111845655-111846048	SK-N-SH_RA	brain:	n/a	chr7:111845904-111845918
18	CTCF	chr7:111845720-111845870	HMEC	breast:	n/a	n/a
19	TEAD4	chr7:111845354-111845914	H1-hESC	embryonic stem cell:	n/a	chr7:111845633-111845642
20	MAX	chr7:111845773-111847521	K562	blood:	n/a	chr7:111846494-111846504
21	PBX3	chr7:111845596-111846890	SK-N-SH	brain:	n/a	n/a
22	MXI1	chr7:111844822-111847472	IMR90	lung:	n/a	n/a
23	SIN3AK20	chr7:111845749-111846939	PANC-1	pancreas:	n/a	n/a
24	SMARCC2	chr7:111845175-111847431	Hela-S3	cervix:	n/a	chr7:111846552-111846561
25	MAX	chr7:111845691-111845930	K562	blood:	n/a	n/a
26	RAD21	chr7:111844971-111847005	H1-hESC	embryonic stem cell:	n/a	chr7:111845990-111846002
27	ELF1	chr7:111845758-111847245	GM12878	blood:	n/a	chr7:111846876-111846885 chr7:111846576-111846585 chr7:111846575-111846586 chr7:111846575-111846586
28	CCNT2	chr7:111845632-111847527	K562	blood:	n/a	n/a
29	RAD21	chr7:111845579-111846065	HepG2	liver:	n/a	chr7:111845990-111846002
30	MXI1	chr7:111843467-111848079	SK-N-SH	brain:	n/a	n/a
31	MAX	chr7:111845247-111847048	SK-N-SH	brain:	n/a	chr7:111846494-111846504
32	ZBTB7A	chr7:111845215-111847079	ECC-1	luminal epithelium:	n/a	n/a
33	SIN3AK20	chr7:111845693-111846029	A549	lung:	n/a	n/a
34	TAF1	chr7:111845445-111845951	Hela-S3	cervix:	n/a	n/a
35	YY1	chr7:111845177-111845915	H1-hESC	embryonic stem cell:	n/a	n/a
36	RAD21	chr7:111845587-111846700	A549	lung:	n/a	chr7:111845990-111846002
37	RAD21	chr7:111845573-111846963	H1-hESC	embryonic stem cell:	n/a	chr7:111845990-111846002
38	MAX	chr7:111845523-111846781	H1-hESC	embryonic stem cell:	n/a	chr7:111846494-111846504
39	REST	chr7:111845729-111846038	SK-N-SH	brain:	n/a	chr7:111846001-111846011 chr7:111845994-111846012
40	MAX	chr7:111845717-111846086	GM12878	blood:	n/a	n/a
41	TCF12	chr7:111845699-111846920	ECC-1	luminal epithelium:	n/a	n/a
42	SIN3AK20	chr7:111845014-111846996	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr7:111845720-111845870	GM12870	blood:	n/a	n/a
44	CHD2	chr7:111845394-111847393	Hela-S3	cervix:	n/a	n/a
45	RFX5	chr7:111845258-111847494	Hela-S3	cervix:	n/a	n/a
46	MXI1	chr7:111844955-111847596	HepG2	liver:	n/a	n/a
47	ZNF263	chr7:111844288-111847502	HEK293-T-REx	kidney:	n/a	chr7:111845191-111845200 chr7:111845576-111845585
48	CHD2	chr7:111845349-111846121	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr7:111845606-111846033	ProgFib	skin:	n/a	n/a
50	POLR2A	chr7:111845718-111847047	Raji	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:111578985..111581380-chr7:111844507..111846039,2	MCF-7	breast:
2	chr7:111814511..111817304-chr7:111843000..111845884,2	K562	blood:
3	chr7:111844189..111846735-chr7:112088922..112092289,7	K562	blood:

Variant related genes	Relation type
ZNF277	TF binding region
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10226284	0.81[CEU][hapmap];0.81[ASN][1000 genomes]
rs10238141	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10247876	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10259741	0.93[ASN][1000 genomes]
rs10266365	0.81[CEU][hapmap]
rs10272126	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10272188	0.90[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10272976	0.80[CHD][hapmap]
rs10953708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10953710	1.00[CEU][hapmap]
rs10953711	1.00[CEU][hapmap]
rs11760599	0.84[EUR][1000 genomes]
rs11761807	1.00[CEU][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11762497	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11763356	0.86[ASN][1000 genomes]
rs11763588	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap]
rs11763768	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11767115	0.93[ASN][1000 genomes]
rs11768608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11768793	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11768891	0.84[CHB][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11769219	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[ASN][1000 genomes]
rs11770767	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11773393	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12666261	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12666328	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12668065	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12673830	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13230061	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs16873374	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159336	1.00[AFR][1000 genomes]
rs17159341	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17159389	1.00[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17159446	1.00[CEU][hapmap]
rs2301725	0.81[CEU][hapmap]
rs2523039	1.00[JPT][hapmap]
rs2708588	0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2708592	0.89[CEU][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2708595	0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2708603	0.89[CEU][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2708604	1.00[JPT][hapmap]
rs3823515	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs41281063	0.80[ASN][1000 genomes]
rs4464880	1.00[CEU][hapmap]
rs4730516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4730517	0.94[ASN][1000 genomes]
rs4730520	0.81[CEU][hapmap];0.81[ASN][1000 genomes]
rs55915049	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56969420	0.83[ASN][1000 genomes]
rs6949164	0.81[CEU][hapmap]
rs6955231	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6966390	0.81[CEU][hapmap]
rs6974364	0.80[CEU][hapmap]
rs6978927	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap]
rs735150	0.88[JPT][hapmap]
rs757196	1.00[CEU][hapmap]
rs7781245	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7792130	0.94[ASN][1000 genomes]
rs7795336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9641480	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9641481	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[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	nsv1021527	chr7:111194596-111851619	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv539086	chr7:111194596-111851619	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv531435	chr7:111333900-111926292	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv491934	chr7:111333900-111975504	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv532335	chr7:111411990-112054905	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3807884	C7orf53	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:111843200-111846800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:111843400-111847200	Active TSS	Brain Hippocampus Middle	brain
3	chr7:111843400-111847400	Active TSS	Brain Cingulate Gyrus	brain
4	chr7:111843400-111847800	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr7:111843600-111847200	Active TSS	Brain Angular Gyrus	brain
6	chr7:111843600-111847600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr7:111843600-111847800	Active TSS	NHLF	lung
8	chr7:111843600-111848400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:111843800-111845800	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr7:111843800-111845800	Flanking Bivalent TSS/Enh	Dnd41	blood
11	chr7:111843800-111846000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:111843800-111847200	Active TSS	Brain Substantia Nigra	brain
13	chr7:111843800-111847200	Active TSS	Fetal Lung	lung
14	chr7:111843800-111847400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr7:111843800-111847400	Active TSS	NHEK	skin
16	chr7:111843800-111847600	Active TSS	Lung	lung
17	chr7:111844000-111845800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr7:111844000-111846000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr7:111844000-111847200	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr7:111844000-111847400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr7:111844000-111847600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr7:111844000-111847600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr7:111844000-111847600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:111844000-111847600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:111844000-111847600	Active TSS	Left Ventricle	heart
26	chr7:111844000-111847800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr7:111844000-111847800	Active TSS	NHDF-Ad	bronchial
28	chr7:111844000-111848000	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr7:111844000-111848000	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr7:111844200-111845800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:111844200-111847200	Active TSS	HUVEC	blood vessel
32	chr7:111844200-111847400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:111844200-111847400	Active TSS	Muscle Satellite Cultured Cells	--
34	chr7:111844200-111847400	Active TSS	Brain Anterior Caudate	brain
35	chr7:111844200-111847400	Active TSS	A549	lung
36	chr7:111844200-111847600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:111844200-111847600	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr7:111844200-111847600	Active TSS	Pancreas	Pancrea
39	chr7:111844200-111847600	Active TSS	Right Ventricle	heart
40	chr7:111844200-111847800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:111844200-111847800	Active TSS	Aorta	Aorta
42	chr7:111844200-111848200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr7:111844400-111846200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr7:111844400-111847400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr7:111844400-111847400	Bivalent/Poised TSS	HepG2	liver
46	chr7:111844400-111847600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr7:111844400-111847600	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr7:111844400-111847600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr7:111844400-111847600	Active TSS	Esophagus	oesophagus
50	chr7:111844400-111847600	Active TSS	Ovary	ovary

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