Variant report

Variant	rs6458956
Chromosome Location	chr6:53659437-53659438
allele	C/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	SMC3	chr6:53659093-53659732	GM12878	blood:	n/a	n/a
2	MYC	chr6:53659365-53659815	HepG2	liver:	n/a	n/a
3	MAX	chr6:53658055-53660083	A549	lung:	n/a	n/a
4	MAX	chr6:53657995-53660610	ECC-1	luminal epithelium:	n/a	chr6:53660589-53660599
5	GABPA	chr6:53659087-53659836	A549	lung:	n/a	n/a
6	TCF12	chr6:53659072-53660088	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr6:53659378-53660349	H1-neurons	neurons:	n/a	n/a
8	YY1	chr6:53659397-53659890	H1-hESC	embryonic stem cell:	n/a	n/a
9	SP1	chr6:53659272-53659948	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3AK20	chr6:53658844-53659455	HepG2	liver:	n/a	n/a
11	POLR2A	chr6:53658319-53660088	GM12878	blood:	n/a	n/a
12	RAD21	chr6:53658987-53659908	ECC-1	luminal epithelium:	n/a	chr6:53659267-53659276
13	POLR2A	chr6:53658017-53660323	H1-hESC	embryonic stem cell:	n/a	n/a
14	REST	chr6:53659119-53659942	HepG2	liver:	n/a	chr6:53659471-53659484
15	SP1	chr6:53658988-53660003	A549	lung:	n/a	n/a
16	ZNF263	chr6:53658118-53660328	HEK293-T-REx	kidney:	n/a	chr6:53659177-53659186
17	MXI1	chr6:53659143-53660047	GM12878	blood:	n/a	n/a
18	SIN3AK20	chr6:53659407-53659765	A549	lung:	n/a	n/a
19	GATA3	chr6:53659199-53659965	A549	lung:	n/a	n/a
20	ELF1	chr6:53659206-53659901	HepG2	liver:	n/a	n/a
21	HA-E2F1	chr6:53658249-53661314	MCF-7	breast:	n/a	chr6:53658580-53658592 chr6:53660791-53660806
22	RAD21	chr6:53658986-53659455	HepG2	liver:	n/a	chr6:53659267-53659276
23	TAF1	chr6:53659253-53660105	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr6:53659157-53659934	GM18505	blood:	n/a	n/a
25	ZEB1	chr6:53659394-53659821	GM12878	blood:	n/a	n/a
26	KAP1	chr6:53659081-53659699	U2OS	brain:	n/a	n/a
27	MAX	chr6:53657848-53661452	HCT-116	colon:	n/a	chr6:53660589-53660599
28	CTCF	chr6:53659100-53659471	H1-hESC	embryonic stem cell:	n/a	n/a
29	TBP	chr6:53658870-53660561	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr6:53659209-53659459	A549	lung:	n/a	n/a
31	MYC	chr6:53658968-53659867	MCF10A-Er-Src	breast:	n/a	n/a
32	RAD21	chr6:53658916-53660298	H1-hESC	embryonic stem cell:	n/a	chr6:53659267-53659276
33	TEAD4	chr6:53658886-53659884	HepG2	liver:	n/a	n/a
34	TAF1	chr6:53659399-53660062	MCF-7	breast:	n/a	n/a
35	POLR2A	chr6:53659104-53660007	Hela-S3	cervix:	n/a	n/a
36	GABPA	chr6:53658939-53659968	HL-60	blood:	n/a	n/a
37	TBP	chr6:53659116-53659746	Hela-S3	cervix:	n/a	n/a
38	ZBTB7A	chr6:53659141-53660958	ECC-1	luminal epithelium:	n/a	n/a
39	TAF1	chr6:53659076-53660060	ECC-1	luminal epithelium:	n/a	n/a
40	GABPA	chr6:53659148-53659851	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr6:53657931-53660001	HepG2	liver:	n/a	n/a
42	SIN3AK20	chr6:53659226-53660120	MCF-7	breast:	n/a	n/a
43	POLR2A	chr6:53658082-53659997	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr6:53659374-53659877	GM12878	blood:	n/a	n/a
45	POLR2A	chr6:53658888-53660073	A549	lung:	n/a	n/a
46	HDAC2	chr6:53658364-53660221	MCF-7	breast:	n/a	chr6:53658736-53658744
47	CTCF	chr6:53659065-53659625	IMR90	lung:	n/a	n/a
48	NRF1	chr6:53658947-53660172	SK-N-SH	brain:	n/a	n/a
49	RAD21	chr6:53659013-53660236	HepG2	liver:	n/a	chr6:53659267-53659276
50	CREB1	chr6:53659242-53659964	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:53656949..53662173-chr6:53781368..53784554,5	MCF-7	breast:
2	chr6:53610265..53615014-chr6:53656858..53662694,9	MCF-7	breast:
3	chr17:57969778..57970541-chr6:53659281..53659963,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	TF binding region
LRRC1	TF binding region
ENSG00000108443	Chromatin interaction
ENSG00000108423	Chromatin interaction
ENSG00000137269	Chromatin interaction
ENSG00000227885	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11759220	0.83[AMR][1000 genomes]
rs11759427	0.80[ASN][1000 genomes]
rs11759473	0.80[ASN][1000 genomes]
rs12662433	0.95[ASN][1000 genomes]
rs3003498	0.83[EUR][1000 genomes]
rs3813850	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4478409	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4645422	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4712042	0.80[ASN][1000 genomes]
rs4715421	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57853292	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs60467893	0.82[EUR][1000 genomes]
rs62397076	0.83[AMR][1000 genomes]
rs62399939	0.99[ASN][1000 genomes]
rs6909040	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7743253	0.83[AMR][1000 genomes]
rs7759593	0.80[ASN][1000 genomes]
rs9463970	0.80[ASN][1000 genomes]
rs9463971	0.95[ASN][1000 genomes]
rs9474643	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv3474747	chr6:53648744-53677210	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3474748	chr6:53648758-53677207	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6458956	LRRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53656800-53661200	Active TSS	Fetal Kidney	kidney
2	chr6:53657400-53661200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:53657400-53661400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:53657600-53659800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:53657600-53661000	Active TSS	H1 Cell Line	embryonic stem cell
6	chr6:53657600-53661000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr6:53657600-53661400	Active TSS	A549	lung
8	chr6:53657800-53659600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr6:53657800-53660200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:53657800-53661000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:53657800-53661600	Active TSS	Fetal Intestine Large	intestine
12	chr6:53657800-53662400	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr6:53658000-53660200	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr6:53658000-53660200	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr6:53658000-53660400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:53658000-53660400	Active TSS	Rectal Smooth Muscle	rectum
17	chr6:53658000-53660600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:53658000-53660600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:53658000-53660600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:53658000-53660800	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr6:53658000-53661000	Active TSS	H9 Cell Line	embryonic stem cell
22	chr6:53658000-53661000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:53658000-53661400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:53658000-53661400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:53658000-53661400	Active TSS	Aorta	Aorta
26	chr6:53658000-53661400	Active TSS	Esophagus	oesophagus
27	chr6:53658000-53661600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:53658000-53661600	Active TSS	Fetal Intestine Small	intestine
29	chr6:53658000-53662000	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr6:53658200-53659600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
31	chr6:53658200-53659600	Flanking Active TSS	HUVEC	blood vessel
32	chr6:53658200-53660200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:53658200-53660200	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr6:53658200-53660400	Active TSS	Left Ventricle	heart
35	chr6:53658200-53660400	Active TSS	Pancreas	Pancrea
36	chr6:53658200-53660600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr6:53658200-53660800	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr6:53658200-53660800	Active TSS	Right Atrium	heart
39	chr6:53658200-53661000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr6:53658200-53661000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:53658200-53661000	Active TSS	Fetal Heart	heart
42	chr6:53658200-53661200	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr6:53658200-53661400	Active TSS	Brain Substantia Nigra	brain
44	chr6:53658200-53661400	Active TSS	Gastric	stomach
45	chr6:53658200-53661400	Active TSS	Ovary	ovary
46	chr6:53658400-53659600	Flanking Active TSS	Liver	Liver
47	chr6:53658400-53660000	Active TSS	Fetal Brain Female	brain
48	chr6:53658400-53660200	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr6:53658400-53661200	Active TSS	HSMM	muscle
50	chr6:53658400-53661400	Active TSS	Stomach Mucosa	stomach

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