Variant report

Variant	rs3813850
Chromosome Location	chr6:53658211-53658212
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	MAX	chr6:53658055-53660083	A549	lung:	n/a	n/a
2	MAX	chr6:53657995-53660610	ECC-1	luminal epithelium:	n/a	chr6:53660589-53660599
3	POLR2A	chr6:53658058-53658723	HepG2	liver:	n/a	n/a
4	MAX	chr6:53657929-53658663	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:53658017-53660323	H1-hESC	embryonic stem cell:	n/a	n/a
6	ZNF263	chr6:53658118-53660328	HEK293-T-REx	kidney:	n/a	chr6:53659177-53659186
7	HNF4A	chr6:53657874-53658711	HepG2	liver:	n/a	chr6:53658179-53658194 chr6:53658179-53658194 chr6:53658180-53658192 chr6:53658179-53658192 chr6:53658179-53658192 chr6:53658180-53658192 chr6:53658179-53658193 chr6:53658175-53658197 chr6:53658179-53658194 chr6:53658180-53658193 chr6:53658178-53658193 chr6:53658185-53658193 chr6:53658179-53658194 chr6:53658179-53658192 chr6:53658179-53658193 chr6:53658177-53658195 chr6:53658181-53658193
8	FOXA1	chr6:53658020-53658421	HepG2	liver:	n/a	n/a
9	ARID3A	chr6:53657660-53658639	HepG2	liver:	n/a	n/a
10	SP1	chr6:53657964-53658937	A549	lung:	n/a	chr6:53658576-53658590
11	MAX	chr6:53657848-53661452	HCT-116	colon:	n/a	chr6:53660589-53660599
12	RCOR1	chr6:53658008-53658551	HepG2	liver:	n/a	n/a
13	POLR2A	chr6:53658172-53658536	HepG2	liver:	n/a	n/a
14	HNF4A	chr6:53657996-53658604	HepG2	liver:	n/a	chr6:53658179-53658194 chr6:53658179-53658194 chr6:53658180-53658192 chr6:53658179-53658192 chr6:53658179-53658192 chr6:53658180-53658192 chr6:53658179-53658193 chr6:53658175-53658197 chr6:53658179-53658194 chr6:53658180-53658193 chr6:53658178-53658193 chr6:53658185-53658193 chr6:53658179-53658194 chr6:53658179-53658192 chr6:53658179-53658193 chr6:53658177-53658195 chr6:53658181-53658193
15	POLR2A	chr6:53657931-53660001	HepG2	liver:	n/a	n/a
16	POLR2A	chr6:53658082-53659997	MCF10A-Er-Src	breast:	n/a	n/a
17	MAFK	chr6:53658065-53658612	HepG2	liver:	n/a	n/a
18	SP1	chr6:53657974-53658699	H1-hESC	embryonic stem cell:	n/a	chr6:53658576-53658590
19	HDAC2	chr6:53657941-53658760	HepG2	liver:	n/a	chr6:53658185-53658193 chr6:53658027-53658041 chr6:53658736-53658744
20	TEAD4	chr6:53657677-53658634	HepG2	liver:	n/a	n/a
21	HEY1	chr6:53657860-53660137	HepG2	liver:	n/a	n/a
22	POLR2A	chr6:53658124-53658891	ECC-1	luminal epithelium:	n/a	n/a
23	SP1	chr6:53657903-53658754	HepG2	liver:	n/a	chr6:53658576-53658590
24	MYBL2	chr6:53657854-53660234	HepG2	liver:	n/a	n/a
25	FOXA2	chr6:53658013-53658381	HepG2	liver:	n/a	n/a
26	ZEB1	chr6:53657986-53661733	HepG2	liver:	n/a	chr6:53660227-53660234 chr6:53660527-53660534 chr6:53660524-53660535
27	POLR2A	chr6:53658096-53660034	ECC-1	luminal epithelium:	n/a	n/a
28	TAF1	chr6:53658065-53660073	H1-hESC	embryonic stem cell:	n/a	n/a
29	HEY1	chr6:53657976-53658779	HepG2	liver:	n/a	n/a
30	CHD1	chr6:53658098-53659003	H1-hESC	embryonic stem cell:	n/a	n/a
31	TEAD4	chr6:53658004-53658348	HepG2	liver:	n/a	n/a
32	SIN3A	chr6:53658117-53661330	H1-hESC	embryonic stem cell:	n/a	chr6:53658947-53658955 chr6:53660236-53660247
33	HNF4G	chr6:53657984-53658732	HepG2	liver:	n/a	chr6:53658179-53658194 chr6:53658179-53658194 chr6:53658180-53658192 chr6:53658179-53658192 chr6:53658179-53658192 chr6:53658180-53658192 chr6:53658179-53658193 chr6:53658175-53658197 chr6:53658179-53658194 chr6:53658180-53658193 chr6:53658185-53658193 chr6:53658179-53658194 chr6:53658179-53658192 chr6:53658179-53658193 chr6:53658177-53658195 chr6:53658181-53658193
34	POLR2A	chr6:53658186-53658745	SK-N-MC	brain:	n/a	n/a
35	REST	chr6:53658031-53658677	HepG2	liver:	n/a	n/a
36	SIN3AK20	chr6:53658042-53661667	MCF-7	breast:	n/a	n/a
37	MBD4	chr6:53657914-53658781	HepG2	liver:	n/a	n/a
38	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
39	RAD21	chr6:53657969-53658717	HepG2	liver:	n/a	n/a
40	TBP	chr6:53658003-53658679	HepG2	liver:	n/a	n/a
41	EP300	chr6:53657949-53658458	HepG2	liver:	n/a	chr6:53658026-53658040
42	MAZ	chr6:53658016-53660357	HepG2	liver:	n/a	n/a
43	MAX	chr6:53657944-53661423	HepG2	liver:	n/a	chr6:53660589-53660599
44	MYC	chr6:53658210-53658219	HepG2	liver:	n/a	n/a
45	MYC	chr6:53658166-53658770	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr6:53657955-53661480	HepG2	liver:	n/a	n/a
47	POLR2A	chr6:53658017-53658789	HepG2	liver:	n/a	n/a
48	NFIC	chr6:53657984-53658698	HepG2	liver:	n/a	n/a
49	HNF4A	chr6:53657904-53658683	HepG2	liver:	n/a	chr6:53658179-53658194 chr6:53658179-53658194 chr6:53658180-53658192 chr6:53658179-53658192 chr6:53658179-53658192 chr6:53658180-53658192 chr6:53658179-53658193 chr6:53658175-53658197 chr6:53658179-53658194 chr6:53658180-53658193 chr6:53658178-53658193 chr6:53658185-53658193 chr6:53658179-53658194 chr6:53658179-53658192 chr6:53658179-53658193 chr6:53658177-53658195 chr6:53658181-53658193
50	TCF12	chr6:53657915-53659917	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	chr6:53655984..53658850-chr6:53782726..53785660,2	MCF-7	breast:
3	chr6:53610265..53615014-chr6:53656858..53662694,9	MCF-7	breast:
4	chr6:53651995..53655009-chr6:53655283..53658516,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL31-2	chr6:53658081-53658505	XLOC_005748
2	lnc-KLHL31-2	chr6:53658081-53658389	XLOC_005748

Variant related genes	Relation type
LRRC1	TF binding region
ENSG00000137269	Chromatin interaction
ENSG00000227885	Chromatin interaction
ENSG00000271218	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11759427	0.93[CHB][hapmap];0.88[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap]
rs12663216	0.81[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap]
rs3003492	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs3003498	0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs4478409	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4486000	0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs4645422	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4715421	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60467893	0.82[EUR][1000 genomes]
rs6458956	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6905563	0.84[CEU][hapmap]
rs6909040	0.80[EUR][1000 genomes]
rs9463970	0.93[CHB][hapmap]
rs9474643	1.00[CHB][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs9474647	0.92[TSI][hapmap]

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
rs3813850	LRRC1	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 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	chr6:53657000-53658600	Weak transcription	Hela-S3	cervix
3	chr6:53657200-53658800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr6:53657400-53661200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:53657400-53661400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:53657600-53659200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:53657600-53659200	Active TSS	Fetal Stomach	stomach
8	chr6:53657600-53659800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:53657600-53661000	Active TSS	H1 Cell Line	embryonic stem cell
10	chr6:53657600-53661000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
11	chr6:53657600-53661400	Active TSS	A549	lung
12	chr6:53657800-53658600	Active TSS	Placenta Amnion	Placenta Amnion
13	chr6:53657800-53658600	Active TSS	NHEK	skin
14	chr6:53657800-53659600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr6:53657800-53660200	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr6:53657800-53661000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:53657800-53661600	Active TSS	Fetal Intestine Large	intestine
18	chr6:53657800-53662400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr6:53658000-53658400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr6:53658000-53658400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:53658000-53658400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
22	chr6:53658000-53658400	Flanking Active TSS	NHLF	lung
23	chr6:53658000-53658600	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr6:53658000-53658600	Active TSS	Fetal Muscle Trunk	muscle
25	chr6:53658000-53658600	Active TSS	Stomach Smooth Muscle	stomach
26	chr6:53658000-53658800	Active TSS	Fetal Lung	lung
27	chr6:53658000-53658800	Active TSS	Right Ventricle	heart
28	chr6:53658000-53659000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:53658000-53659000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:53658000-53659000	Flanking Active TSS	Fetal Thymus	thymus
31	chr6:53658000-53659200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr6:53658000-53659200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr6:53658000-53659200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr6:53658000-53659200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
35	chr6:53658000-53659200	Flanking Active TSS	NH-A	brain
36	chr6:53658000-53659400	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr6:53658000-53660200	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr6:53658000-53660200	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr6:53658000-53660400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:53658000-53660400	Active TSS	Rectal Smooth Muscle	rectum
41	chr6:53658000-53660600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:53658000-53660600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:53658000-53660600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:53658000-53660800	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr6:53658000-53661000	Active TSS	H9 Cell Line	embryonic stem cell
46	chr6:53658000-53661000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:53658000-53661400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:53658000-53661400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:53658000-53661400	Active TSS	Aorta	Aorta
50	chr6:53658000-53661400	Active TSS	Esophagus	oesophagus

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