Variant report

Variant	rs4947012
Chromosome Location	chr6:110012274-110012275
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	POLR2A	chr6:110012145-110012895	MCF-7	breast:	n/a	n/a
2	CREB1	chr6:110012032-110012949	HepG2	liver:	n/a	n/a
3	RFX5	chr6:110011683-110012629	HepG2	liver:	n/a	chr6:110011737-110011752 chr6:110011741-110011750
4	YY1	chr6:110012143-110012801	K562	blood:	n/a	chr6:110012340-110012362 chr6:110012726-110012737
5	CHD1	chr6:110011967-110012344	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:110011987-110012705	GM12878	blood:	n/a	n/a
7	MYC	chr6:110011766-110012625	H1-hESC	embryonic stem cell:	n/a	n/a
8	NFIC	chr6:110012116-110012732	HepG2	liver:	n/a	n/a
9	WRNIP1	chr6:110011933-110012956	GM12878	blood:	n/a	n/a
10	MTA3	chr6:110011802-110013073	GM12878	blood:	n/a	n/a
11	TAF1	chr6:110011912-110012667	H1-neurons	neurons:	n/a	n/a
12	GTF2F1	chr6:110011928-110012631	Hela-S3	cervix:	n/a	n/a
13	SPI1	chr6:110012249-110012479	GM12891	blood:	n/a	chr6:110012257-110012270 chr6:110012368-110012375
14	YY1	chr6:110012111-110012707	HCT-116	colon:	n/a	chr6:110012340-110012362
15	CHD2	chr6:110011510-110012632	H1-hESC	embryonic stem cell:	n/a	n/a
16	SMARCB1	chr6:110011591-110012953	Hela-S3	cervix:	n/a	n/a
17	YY1	chr6:110012253-110012492	K562	blood:	n/a	chr6:110012340-110012362
18	POLR2A	chr6:110011904-110012898	H1-neurons	neurons:	n/a	n/a
19	POLR2A	chr6:110011980-110012731	GM12892	blood:	n/a	n/a
20	YY1	chr6:110012172-110012650	GM12891	blood:	n/a	chr6:110012340-110012362
21	KAP1	chr6:110011956-110012722	U2OS	brain:	n/a	n/a
22	MAX	chr6:110011632-110013021	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr6:110012204-110012646	GM12891	blood:	n/a	n/a
24	SPI1	chr6:110012067-110012893	HL-60	blood:	n/a	chr6:110012257-110012270 chr6:110012368-110012375 chr6:110012801-110012808 chr6:110012786-110012799 chr6:110012792-110012805
25	POLR2A	chr6:110011880-110012799	H1-hESC	embryonic stem cell:	n/a	n/a
26	CREB1	chr6:110012151-110012951	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAX	chr6:110011615-110012615	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:110011868-110012787	PANC-1	pancreas:	n/a	n/a
29	EP300	chr6:110012198-110012640	SK-N-SH_RA	brain:	n/a	n/a
30	POLR2A	chr6:110011677-110012885	HUVEC	blood vessel:	n/a	n/a
31	SP4	chr6:110011985-110012664	H1-hESC	embryonic stem cell:	n/a	chr6:110012319-110012330 chr6:110012448-110012464
32	SP1	chr6:110012017-110012694	H1-hESC	embryonic stem cell:	n/a	chr6:110012451-110012461 chr6:110012319-110012330 chr6:110012468-110012477 chr6:110012467-110012479 chr6:110012469-110012478 chr6:110012452-110012461 chr6:110012464-110012478 chr6:110012450-110012462 chr6:110012452-110012461 chr6:110012447-110012461 chr6:110012451-110012460 chr6:110012451-110012461 chr6:110012450-110012462
33	CUX1	chr6:110012038-110012830	K562	blood:	n/a	n/a
34	ARID3A	chr6:110011916-110012560	HepG2	liver:	n/a	n/a
35	SIN3AK20	chr6:110011884-110012921	SK-N-SH	brain:	n/a	n/a
36	FOS	chr6:110012258-110012507	MCF10A-Er-Src	breast:	n/a	n/a
37	ELF1	chr6:110012114-110012855	GM12878	blood:	n/a	chr6:110012727-110012739 chr6:110012365-110012378
38	POLR2A	chr6:110011630-110012990	GM18505	blood:	n/a	n/a
39	POLR2A	chr6:110011899-110012908	U87	brain:	n/a	n/a
40	SIN3A	chr6:110011677-110012776	GM12878	blood:	n/a	chr6:110012719-110012730
41	ETS1	chr6:110012063-110012763	GM12878	blood:	n/a	n/a
42	YY1	chr6:110011869-110012882	HepG2	liver:	n/a	chr6:110012340-110012362 chr6:110012726-110012737
43	YY1	chr6:110012137-110012553	A549	lung:	n/a	chr6:110012340-110012362
44	POLR2A	chr6:110011905-110012902	U87	brain:	n/a	n/a
45	CREB1	chr6:110012273-110012709	A549	lung:	n/a	n/a
46	YY1	chr6:110011951-110012631	HepG2	liver:	n/a	chr6:110012340-110012362
47	POLR2A	chr6:110012057-110012764	HCT-116	colon:	n/a	n/a
48	EBF1	chr6:110011507-110012643	GM12878	blood:	n/a	chr6:110011711-110011720 chr6:110011709-110011720
49	RELA	chr6:110011810-110012983	GM18951	blood:	n/a	n/a
50	ZNF384	chr6:110012208-110012915	K562	blood:	n/a	chr6:110012313-110012321

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:110012263-110012313	HepG2	liver:	n/a
2	chr6:110012263-110012313	ovcar-3	ovarian:	n/a
3	chr6:110012263-110012313	HMEC	breast:	n/a
4	chr6:110012263-110012313	HL-60	blood:	n/a
5	chr6:110012263-110012313	NB4	blood:	n/a
6	chr6:110012263-110012313	U87	brain:	n/a
7	chr6:110012263-110012313	AG09309	skin:	n/a
8	chr6:110012263-110012313	ProgFib	skin:	n/a
9	chr6:110012263-110012313	T-47D	breast:	n/a
10	chr6:110012263-110012313	HCT-116	colon:	n/a
11	chr6:110012263-110012313	HCM	heart:	n/a
12	chr6:110012263-110012313	GM12878	blood:	n/a
13	chr6:110012263-110012313	GM12892	blood:	n/a
14	chr6:110012263-110012313	NT2-D1	testis:	n/a
15	chr6:110012263-110012313	Hela-S3	cervix:	n/a
16	chr6:110012263-110012313	AG09319	gingival:	n/a
17	chr6:110012263-110012313	AG04449	skin:	fetal
18	chr6:110012263-110012313	HRE	kidney:	n/a
19	chr6:110012263-110012313	HRCEpiC	kidney:	n/a
20	chr6:110012263-110012313	HCPEpiC	choroid plexus:	n/a
21	chr6:110012263-110012313	BJ	skin:	n/a
22	chr6:110012263-110012313	PFSK-1	brain:	n/a
23	chr6:110012263-110012313	GM19239	blood:	n/a
24	chr6:110012263-110012313	HUVEC	blood vessel:	n/a
25	chr6:110012263-110012313	ECC-1	luminal epithelium:	n/a
26	chr6:110012263-110012313	SKMC	muscle:	n/a
27	chr6:110012263-110012313	HAEpiC	amniotic membrane:	n/a
28	chr6:110012263-110012313	PANC-1	pancreas:	n/a
29	chr6:110012263-110012313	HEK293	kidney:	embryo
30	chr6:110012263-110012313	GM12891	blood:	n/a
31	chr6:110012263-110012313	BE2_C	brain:	n/a
32	chr6:110012263-110012313	AG10803	skin:	n/a
33	chr6:110012263-110012313	AoSMC	blood vessel:	n/a
34	chr6:110012263-110012313	GM06990	blood:	n/a
35	chr6:110012263-110012313	SK-N-SH_RA	brain:	n/a
36	chr6:110012263-110012313	HPAEpiC	pulmonary alveolar:	n/a
37	chr6:110012263-110012313	HCF	heart:	n/a
38	chr6:110012263-110012313	SK-N-SH	brain:	n/a
39	chr6:110012263-110012313	Hepatocyte	liver:	n/a
40	chr6:110012263-110012313	SAEC	small airway:	n/a
41	chr6:110012263-110012313	MCF-7	breast:	n/a
42	chr6:110012263-110012313	Jurkat	blood:	n/a
43	chr6:110012263-110012313	LNCaP	prostate:	n/a
44	chr6:110012263-110012313	NH-A	brain:	n/a
45	chr6:110012263-110012313	HEEpiC	esophagus:	n/a
46	chr6:110012263-110012313	RPTEC	kidney:	n/a
47	chr6:110012263-110012313	HRPEpiC	eye:	n/a
48	chr6:110012263-110012313	SK-N-MC	brain:	n/a
49	chr6:110012263-110012313	AG04450	lung:	fetal
50	chr6:110012263-110012313	HNPCEpiC	eye:	n/a

Variant related genes	Relation type
FIG4	TF binding region
AK9	TF binding region
FIG4	CpG island
AK9	CpG island

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1590186	1.00[ASN][1000 genomes]
rs17602109	1.00[ASN][1000 genomes]
rs1998813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4947018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55895756	0.95[EUR][1000 genomes]
rs56107923	0.95[EUR][1000 genomes]
rs56378532	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7454802	0.95[EUR][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	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv933105	chr6:109933270-110064342	ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv817322	chr6:109933272-110070574	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv830769	chr6:109944334-110078120	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv604485	chr6:109959269-110054486	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4947012	RP11-425D10.10	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110010800-110013600	Active TSS	Stomach Smooth Muscle	stomach
2	chr6:110011000-110013000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:110011000-110013400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr6:110011000-110013600	Active TSS	H1 Cell Line	embryonic stem cell
5	chr6:110011000-110013600	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:110011000-110013600	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr6:110011000-110013800	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr6:110011200-110012800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:110011200-110012800	Active TSS	Duodenum Mucosa	Duodenum
10	chr6:110011200-110013000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:110011200-110013000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:110011200-110013000	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr6:110011200-110013000	Active TSS	Brain Anterior Caudate	brain
14	chr6:110011200-110013000	Active TSS	Colon Smooth Muscle	Colon
15	chr6:110011200-110013000	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr6:110011200-110013200	Active TSS	Brain Cingulate Gyrus	brain
17	chr6:110011200-110013200	Active TSS	Fetal Brain Male	brain
18	chr6:110011200-110013200	Active TSS	Fetal Intestine Small	intestine
19	chr6:110011200-110013200	Active TSS	Psoas Muscle	Psoas
20	chr6:110011200-110013400	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr6:110011200-110013400	Active TSS	NHLF	lung
22	chr6:110011200-110013600	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr6:110011200-110013600	Active TSS	Fetal Kidney	kidney
24	chr6:110011200-110015000	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr6:110011400-110012400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr6:110011400-110012400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:110011400-110012600	Active TSS	Right Atrium	heart
28	chr6:110011400-110012800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:110011400-110012800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:110011400-110012800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:110011400-110012800	Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr6:110011400-110012800	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr6:110011400-110012800	Active TSS	Brain Substantia Nigra	brain
34	chr6:110011400-110012800	Active TSS	Left Ventricle	heart
35	chr6:110011400-110012800	Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr6:110011400-110012800	Active TSS	K562	blood
37	chr6:110011400-110013000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:110011400-110013000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:110011400-110013000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:110011400-110013000	Active TSS	Fetal Heart	heart
41	chr6:110011400-110013000	Active TSS	Fetal Lung	lung
42	chr6:110011400-110013000	Active TSS	Gastric	stomach
43	chr6:110011400-110013000	Active TSS	Pancreas	Pancrea
44	chr6:110011400-110013000	Active TSS	Rectal Mucosa Donor 31	rectum
45	chr6:110011400-110013000	Active TSS	Right Ventricle	heart
46	chr6:110011400-110013000	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr6:110011400-110013000	Active TSS	Small Intestine	intestine
48	chr6:110011400-110013000	Active TSS	Stomach Mucosa	stomach
49	chr6:110011400-110013000	Active TSS	HSMMtube	muscle
50	chr6:110011400-110013200	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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