Variant report

Variant	rs3003498
Chromosome Location	chr6:53663882-53663883
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:53663860-53663910	RPTEC	kidney:	n/a
2	chr6:53663860-53663910	HCF	heart:	n/a
3	chr6:53663860-53663910	AG09309	skin:	n/a
4	chr6:53663860-53663910	HUVEC	blood vessel:	n/a
5	chr6:53663860-53663910	BJ	skin:	n/a
6	chr6:53663860-53663910	GM12891	blood:	n/a
7	chr6:53663860-53663910	AG09319	gingival:	n/a
8	chr6:53663860-53663910	AoSMC	blood vessel:	n/a
9	chr6:53663860-53663910	Hepatocyte	liver:	n/a
10	chr6:53663860-53663910	BE2_C	brain:	n/a
11	chr6:53663860-53663910	HAEpiC	amniotic membrane:	n/a
12	chr6:53663860-53663910	HCM	heart:	n/a
13	chr6:53663860-53663910	NB4	blood:	n/a
14	chr6:53663860-53663910	MCF10A-Er-Src	breast:	n/a
15	chr6:53663860-53663910	PFSK-1	brain:	n/a
16	chr6:53663860-53663910	IMR90	lung:	fetal
17	chr6:53663860-53663910	GM06990	blood:	n/a
18	chr6:53663860-53663910	PANC-1	pancreas:	n/a
19	chr6:53663860-53663910	NT2-D1	testis:	n/a
20	chr6:53663860-53663910	HRCEpiC	kidney:	n/a
21	chr6:53663860-53663910	SK-N-SH_RA	brain:	n/a
22	chr6:53663860-53663910	HMEC	breast:	n/a
23	chr6:53663860-53663910	MCF-7	breast:	n/a
24	chr6:53663860-53663910	H1-hESC	embryonic stem cell:	embryo
25	chr6:53663860-53663910	SAEC	small airway:	n/a
26	chr6:53663860-53663910	AG04449	skin:	fetal
27	chr6:53663860-53663910	SKMC	muscle:	n/a
28	chr6:53663860-53663910	Caco-2	colon:	n/a
29	chr6:53663860-53663910	HNPCEpiC	eye:	n/a
30	chr6:53663860-53663910	NH-A	brain:	n/a
31	chr6:53663860-53663910	U87	brain:	n/a
32	chr6:53663860-53663910	NHDF-neo	bronchial:	n/a
33	chr6:53663860-53663910	HRPEpiC	eye:	n/a
34	chr6:53663860-53663910	NHBE	bronchial:	n/a
35	chr6:53663860-53663910	GM19239	blood:	n/a
36	chr6:53663860-53663910	AG04450	lung:	fetal
37	chr6:53663860-53663910	SK-N-MC	brain:	n/a
38	chr6:53663860-53663910	HRE	kidney:	n/a
39	chr6:53663860-53663910	ovcar-3	ovarian:	n/a
40	chr6:53663860-53663910	Jurkat	blood:	n/a
41	chr6:53663860-53663910	GM12892	blood:	n/a
42	chr6:53663860-53663910	HCPEpiC	choroid plexus:	n/a
43	chr6:53663860-53663910	HIPEpiC	eye:	n/a
44	chr6:53663860-53663910	ProgFib	skin:	n/a
45	chr6:53663860-53663910	CMK	blood:	n/a
46	chr6:53663860-53663910	LNCaP	prostate:	n/a
47	chr6:53663860-53663910	HL-60	blood:	n/a
48	chr6:53663860-53663910	K562	blood:	n/a
49	chr6:53663860-53663910	Hela-S3	cervix:	n/a
50	chr6:53663860-53663910	SK-N-SH	brain:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53663341..53666059-chr6:53671400..53673766,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228614	CpG island

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11759220	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11759427	0.83[GIH][hapmap];0.87[MEX][hapmap]
rs12661475	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12661938	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12663216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1883632	0.89[CHB][hapmap]
rs3001004	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3001005	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3001006	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3001007	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3001008	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3003488	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3003490	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3003492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3003494	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3813850	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]
rs4254992	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4273680	0.85[CHD][hapmap];0.80[JPT][hapmap]
rs4478409	0.86[JPT][hapmap]
rs4486000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4540263	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4582388	0.83[ASN][1000 genomes]
rs4618525	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4640878	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4645422	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4715427	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4715429	0.81[ASN][1000 genomes]
rs60467893	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62397076	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62397090	0.94[EUR][1000 genomes]
rs6458956	0.83[EUR][1000 genomes]
rs6905323	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6905563	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6906326	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs6909040	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6909094	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6925391	0.81[ASN][1000 genomes]
rs7750173	0.91[EUR][1000 genomes]
rs9296720	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9463983	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9463988	0.81[ASN][1000 genomes]
rs9463996	0.94[JPT][hapmap]
rs9463997	0.84[CHD][hapmap];0.89[JPT][hapmap]
rs9474643	0.82[CHB][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap]
rs9474661	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9474665	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3003498	LRRC1	Cis_1M	lymphoblastoid	RTeQTL
rs3003498	C6orf142	cis	cerebellum	SCAN
rs3003498	BCL7A	trans	lymphoblastoid	seeQTL
rs3003498	BAG2	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53666400	Weak transcription	Primary B cells from cord blood	blood
2	chr6:53661400-53666600	Weak transcription	Aorta	Aorta
3	chr6:53661400-53667200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:53661400-53668000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:53661400-53668000	Weak transcription	Ovary	ovary
6	chr6:53661400-53669800	Weak transcription	Gastric	stomach
7	chr6:53661400-53670400	Weak transcription	Primary T cells from cord blood	blood
8	chr6:53661400-53675600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
10	chr6:53661600-53664000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:53661600-53665000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:53661600-53665800	Weak transcription	NHLF	lung
13	chr6:53661800-53664000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:53662000-53670200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:53662200-53665800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:53662200-53667200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:53662400-53664000	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:53662400-53664200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr6:53662400-53664600	Weak transcription	Brain Substantia Nigra	brain
20	chr6:53662400-53667400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:53662400-53668000	Weak transcription	NH-A	brain
22	chr6:53662600-53664000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:53662600-53664200	Weak transcription	Hela-S3	cervix
24	chr6:53662600-53664800	Enhancers	HepG2	liver
25	chr6:53662600-53665800	Weak transcription	Brain Anterior Caudate	brain
26	chr6:53662600-53666800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr6:53662600-53666800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr6:53662600-53668000	Weak transcription	Pancreas	Pancrea
29	chr6:53662600-53669600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:53662600-53670000	Weak transcription	Esophagus	oesophagus
31	chr6:53662600-53670400	Weak transcription	Thymus	Thymus
32	chr6:53662600-53677600	Weak transcription	Small Intestine	intestine
33	chr6:53662800-53667800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr6:53662800-53668000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:53662800-53668000	Weak transcription	NHEK	skin
36	chr6:53662800-53669800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:53662800-53669800	Weak transcription	HMEC	breast
38	chr6:53662800-53670200	Weak transcription	Fetal Intestine Large	intestine
39	chr6:53662800-53670200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr6:53662800-53675400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr6:53663000-53664000	Weak transcription	Brain Hippocampus Middle	brain
42	chr6:53663000-53664400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:53663000-53669800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:53663200-53670600	Weak transcription	Fetal Intestine Small	intestine
45	chr6:53663400-53664800	Enhancers	Fetal Thymus	thymus
46	chr6:53663600-53664000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr6:53663600-53664000	Enhancers	Colonic Mucosa	Colon
48	chr6:53663600-53664000	Enhancers	HUVEC	blood vessel
49	chr6:53663600-53664200	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr6:53663600-53664800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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