Variant report

Variant	rs4645422
Chromosome Location	chr6:53660557-53660558
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	MAX	chr6:53657995-53660610	ECC-1	luminal epithelium:	n/a	chr6:53660589-53660599
2	GATA3	chr6:53660389-53661336	MCF-7	breast:	n/a	chr6:53660700-53660708
3	HA-E2F1	chr6:53658249-53661314	MCF-7	breast:	n/a	chr6:53658580-53658592 chr6:53660791-53660806
4	MAX	chr6:53657848-53661452	HCT-116	colon:	n/a	chr6:53660589-53660599
5	TBP	chr6:53658870-53660561	H1-hESC	embryonic stem cell:	n/a	n/a
6	SIN3AK20	chr6:53660373-53660946	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZBTB7A	chr6:53659141-53660958	ECC-1	luminal epithelium:	n/a	n/a
8	GATA3	chr6:53660472-53661232	T-47D	breast:	n/a	chr6:53660700-53660708
9	MAZ	chr6:53658285-53661262	IMR90	lung:	n/a	chr6:53660589-53660599
10	ZEB1	chr6:53657986-53661733	HepG2	liver:	n/a	chr6:53660227-53660234 chr6:53660527-53660534 chr6:53660524-53660535
11	ZBTB7A	chr6:53659259-53660971	ECC-1	luminal epithelium:	n/a	n/a
12	SIN3A	chr6:53658117-53661330	H1-hESC	embryonic stem cell:	n/a	chr6:53658947-53658955 chr6:53660236-53660247
13	SIN3AK20	chr6:53658042-53661667	MCF-7	breast:	n/a	n/a
14	EGR1	chr6:53658127-53661147	HCT-116	colon:	n/a	chr6:53659819-53659833 chr6:53660784-53660793 chr6:53660781-53660794 chr6:53659793-53659807 chr6:53660041-53660055 chr6:53660781-53660794 chr6:53660783-53660793 chr6:53660781-53660794
15	HCFC1	chr6:53658945-53660683	Hela-S3	cervix:	n/a	n/a
16	MAX	chr6:53657944-53661423	HepG2	liver:	n/a	chr6:53660589-53660599
17	MAX	chr6:53660542-53661281	H1-hESC	embryonic stem cell:	n/a	chr6:53660589-53660599
18	POLR2A	chr6:53657955-53661480	HepG2	liver:	n/a	n/a
19	REST	chr6:53659269-53660838	H1-neurons	neurons:	n/a	chr6:53659471-53659484 chr6:53660238-53660256 chr6:53660817-53660830
20	E2F4	chr6:53660248-53660610	MCF10A-Er-Src	breast:	n/a	n/a
21	MAX	chr6:53657973-53661406	HCT-116	colon:	n/a	chr6:53660589-53660599
22	CTBP2	chr6:53658435-53661168	H1-hESC	embryonic stem cell:	n/a	n/a
23	ZNF263	chr6:53660548-53661520	HEK293-T-REx	kidney:	n/a	n/a
24	MAX	chr6:53660478-53661404	MCF-7	breast:	n/a	chr6:53660589-53660599
25	ZEB1	chr6:53660554-53661618	HepG2	liver:	n/a	n/a
26	SMARCB1	chr6:53658842-53660797	Hela-S3	cervix:	n/a	n/a
27	NR2F2	chr6:53660324-53661236	MCF-7	breast:	n/a	n/a
28	MAX	chr6:53660299-53661293	MCF-7	breast:	n/a	chr6:53660589-53660599
29	MYC	chr6:53660276-53660589	MCF10A-Er-Src	breast:	n/a	n/a
30	SIN3AK20	chr6:53660343-53661350	MCF-7	breast:	n/a	n/a
31	RCOR1	chr6:53658119-53661488	IMR90	lung:	n/a	n/a
32	EGR1	chr6:53660521-53660976	MCF-7	breast:	n/a	chr6:53660784-53660793 chr6:53660781-53660794 chr6:53660781-53660794 chr6:53660783-53660793 chr6:53660781-53660794
33	RCOR1	chr6:53660524-53660974	HepG2	liver:	n/a	n/a
34	USF2	chr6:53660404-53660573	Hela-S3	cervix:	n/a	n/a
35	EGR1	chr6:53659091-53661097	HCT-116	colon:	n/a	chr6:53659819-53659833 chr6:53660784-53660793 chr6:53660781-53660794 chr6:53659793-53659807 chr6:53660041-53660055 chr6:53660781-53660794 chr6:53660783-53660793 chr6:53660781-53660794
36	GATA3	chr6:53660332-53661316	MCF-7	breast:	n/a	chr6:53660700-53660708

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:53660548-53660598	HEK293	kidney:	embryo
2	chr6:53660548-53660598	ovcar-3	ovarian:	n/a
3	chr6:53660548-53660598	AG04450	lung:	fetal
4	chr6:53660548-53660598	H1-hESC	embryonic stem cell:	embryo
5	chr6:53660548-53660598	AG09309	skin:	n/a
6	chr6:53660548-53660598	LNCaP	prostate:	n/a
7	chr6:53660548-53660598	Caco-2	colon:	n/a
8	chr6:53660548-53660598	BE2_C	brain:	n/a
9	chr6:53660548-53660598	NB4	blood:	n/a
10	chr6:53660548-53660598	IMR90	lung:	fetal
11	chr6:53660548-53660598	PrEC	prostate:	n/a
12	chr6:53660548-53660598	Jurkat	blood:	n/a
13	chr6:53660548-53660598	RPTEC	kidney:	n/a
14	chr6:53660548-53660598	PFSK-1	brain:	n/a
15	chr6:53660548-53660598	K562	blood:	n/a
16	chr6:53660548-53660598	HCM	heart:	n/a
17	chr6:53660548-53660598	HCT-116	colon:	n/a
18	chr6:53660548-53660598	NH-A	brain:	n/a
19	chr6:53660548-53660598	PANC-1	pancreas:	n/a
20	chr6:53660548-53660598	HEEpiC	esophagus:	n/a
21	chr6:53660548-53660598	AG09319	gingival:	n/a
22	chr6:53660548-53660598	HMEC	breast:	n/a
23	chr6:53660548-53660598	BJ	skin:	n/a
24	chr6:53660548-53660598	T-47D	breast:	n/a
25	chr6:53660548-53660598	NHDF-neo	bronchial:	n/a
26	chr6:53660548-53660598	GM12891	blood:	n/a
27	chr6:53660548-53660598	NT2-D1	testis:	n/a
28	chr6:53660548-53660598	SK-N-MC	brain:	n/a
29	chr6:53660548-53660598	CMK	blood:	n/a
30	chr6:53660548-53660598	Hepatocyte	liver:	n/a
31	chr6:53660548-53660598	HRPEpiC	eye:	n/a
32	chr6:53660548-53660598	NHBE	bronchial:	n/a
33	chr6:53660548-53660598	U87	brain:	n/a
34	chr6:53660548-53660598	SK-N-SH	brain:	n/a
35	chr6:53660548-53660598	MCF-7	breast:	n/a
36	chr6:53660548-53660598	HepG2	liver:	n/a
37	chr6:53660548-53660598	AoSMC	blood vessel:	n/a
38	chr6:53660548-53660598	GM19239	blood:	n/a
39	chr6:53660548-53660598	HCF	heart:	n/a
40	chr6:53660548-53660598	SAEC	small airway:	n/a
41	chr6:53660548-53660598	ProgFib	skin:	n/a
42	chr6:53660548-53660598	ECC-1	luminal epithelium:	n/a
43	chr6:53660548-53660598	HNPCEpiC	eye:	n/a
44	chr6:53660548-53660598	HRCEpiC	kidney:	n/a
45	chr6:53660548-53660598	A549	lung:	n/a
46	chr6:53660548-53660598	GM12878	blood:	n/a
47	chr6:53660548-53660598	SK-N-SH_RA	brain:	n/a
48	chr6:53660548-53660598	GM12892	blood:	n/a
49	chr6:53660548-53660598	AG10803	skin:	n/a
50	chr6:53660548-53660598	HAEpiC	amniotic membrane:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:53656949..53662173-chr6:53781368..53784554,5	MCF-7	breast:
2	chr6:53660354..53661152-chr6:53734380..53735119,2	MCF-7	breast:
3	chr6:53610265..53615014-chr6:53656858..53662694,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	TF binding region
ENSG00000228614	CpG island
ENSG00000137269	Chromatin interaction
ENSG00000227885	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11759220	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12661475	0.80[EUR][1000 genomes]
rs12663216	0.80[EUR][1000 genomes]
rs3001004	0.80[EUR][1000 genomes]
rs3001005	0.80[EUR][1000 genomes]
rs3001006	0.80[EUR][1000 genomes]
rs3001007	0.80[EUR][1000 genomes]
rs3001008	0.80[EUR][1000 genomes]
rs3003488	0.80[EUR][1000 genomes]
rs3003490	0.80[EUR][1000 genomes]
rs3003492	0.80[EUR][1000 genomes]
rs3003494	0.80[EUR][1000 genomes]
rs3003498	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3813850	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4254992	0.80[EUR][1000 genomes]
rs4486000	0.80[EUR][1000 genomes]
rs4618525	0.80[EUR][1000 genomes]
rs4640878	0.80[EUR][1000 genomes]
rs4715421	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59378492	0.83[AFR][1000 genomes]
rs60295192	0.81[AFR][1000 genomes]
rs60467893	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62397076	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6458956	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6905563	0.80[EUR][1000 genomes]
rs6909040	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6909094	0.80[EUR][1000 genomes]
rs9296720	0.80[EUR][1000 genomes]
rs9474661	0.80[EUR][1000 genomes]
rs9474665	0.80[EUR][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
rs4645422	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	chr6:53657600-53661000	Active TSS	H1 Cell Line	embryonic stem cell
5	chr6:53657600-53661000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:53657600-53661400	Active TSS	A549	lung
7	chr6:53657800-53661000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:53657800-53661600	Active TSS	Fetal Intestine Large	intestine
9	chr6:53657800-53662400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr6:53658000-53660600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:53658000-53660600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:53658000-53660600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:53658000-53660800	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr6:53658000-53661000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr6:53658000-53661000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:53658000-53661400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:53658000-53661400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:53658000-53661400	Active TSS	Aorta	Aorta
19	chr6:53658000-53661400	Active TSS	Esophagus	oesophagus
20	chr6:53658000-53661600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:53658000-53661600	Active TSS	Fetal Intestine Small	intestine
22	chr6:53658000-53662000	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr6:53658200-53660600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:53658200-53660800	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr6:53658200-53660800	Active TSS	Right Atrium	heart
26	chr6:53658200-53661000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr6:53658200-53661000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:53658200-53661000	Active TSS	Fetal Heart	heart
29	chr6:53658200-53661200	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr6:53658200-53661400	Active TSS	Brain Substantia Nigra	brain
31	chr6:53658200-53661400	Active TSS	Gastric	stomach
32	chr6:53658200-53661400	Active TSS	Ovary	ovary
33	chr6:53658400-53661200	Active TSS	HSMM	muscle
34	chr6:53658400-53661400	Active TSS	Stomach Mucosa	stomach
35	chr6:53658400-53661400	Active TSS	NHLF	lung
36	chr6:53658600-53660600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:53658600-53660800	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr6:53658600-53661000	Active TSS	Brain Angular Gyrus	brain
39	chr6:53658600-53661000	Active TSS	Brain Anterior Caudate	brain
40	chr6:53658600-53661000	Bivalent/Poised TSS	HepG2	liver
41	chr6:53658600-53661800	Active TSS	Brain Hippocampus Middle	brain
42	chr6:53658800-53661000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:53658800-53661000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:53658800-53661000	Active TSS	Small Intestine	intestine
45	chr6:53658800-53661400	Active TSS	Colon Smooth Muscle	Colon
46	chr6:53659000-53660800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:53659000-53661000	Active TSS	Thymus	Thymus
48	chr6:53659000-53661200	Active TSS	Brain Cingulate Gyrus	brain
49	chr6:53659000-53661200	Active TSS	Placenta Amnion	Placenta Amnion
50	chr6:53659000-53661200	Active TSS	NHEK	skin

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