Variant report

Variant	rs34113003
Chromosome Location	chr6:53659234-53659235
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	SMC3	chr6:53659093-53659732	GM12878	blood:	n/a	n/a
2	MAX	chr6:53658055-53660083	A549	lung:	n/a	n/a
3	CTCF	chr6:53659148-53659357	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr6:53659200-53659350	GM12878	blood:	n/a	n/a
5	CTCF	chr6:53659160-53659371	GM12892	blood:	n/a	n/a
6	CTCF	chr6:53659150-53659412	HepG2	liver:	n/a	n/a
7	MAX	chr6:53657995-53660610	ECC-1	luminal epithelium:	n/a	chr6:53660589-53660599
8	GABPA	chr6:53659087-53659836	A549	lung:	n/a	n/a
9	TCF12	chr6:53659072-53660088	ECC-1	luminal epithelium:	n/a	n/a
10	CTCF	chr6:53659160-53659310	AG10803	skin:	n/a	n/a
11	SIN3AK20	chr6:53658844-53659455	HepG2	liver:	n/a	n/a
12	CTCF	chr6:53659160-53659310	HCPEpiC	choroid plexus:	n/a	n/a
13	POLR2A	chr6:53658319-53660088	GM12878	blood:	n/a	n/a
14	RAD21	chr6:53658987-53659908	ECC-1	luminal epithelium:	n/a	chr6:53659267-53659276
15	POLR2A	chr6:53658017-53660323	H1-hESC	embryonic stem cell:	n/a	n/a
16	REST	chr6:53659119-53659942	HepG2	liver:	n/a	chr6:53659471-53659484
17	CTCF	chr6:53659182-53659352	Spleen_OC	spleen:	n/a	n/a
18	SP1	chr6:53658988-53660003	A549	lung:	n/a	n/a
19	ZNF263	chr6:53658118-53660328	HEK293-T-REx	kidney:	n/a	chr6:53659177-53659186
20	MXI1	chr6:53659143-53660047	GM12878	blood:	n/a	n/a
21	CTCF	chr6:53659160-53659310	GM12872	blood:	n/a	n/a
22	CTCF	chr6:53659140-53659290	GM12867	blood:	n/a	n/a
23	GATA3	chr6:53659199-53659965	A549	lung:	n/a	n/a
24	CTCF	chr6:53659140-53659290	HBMEC	blood vessel:	n/a	n/a
25	ELF1	chr6:53659206-53659901	HepG2	liver:	n/a	n/a
26	HA-E2F1	chr6:53658249-53661314	MCF-7	breast:	n/a	chr6:53658580-53658592 chr6:53660791-53660806
27	CTCF	chr6:53659141-53659367	LNCaP	prostate:	n/a	n/a
28	RAD21	chr6:53658986-53659455	HepG2	liver:	n/a	chr6:53659267-53659276
29	CTCF	chr6:53659160-53659310	GM12864	blood:	n/a	n/a
30	POLR2A	chr6:53659157-53659934	GM18505	blood:	n/a	n/a
31	CTCF	chr6:53659120-53659270	RPTEC	kidney:	n/a	n/a
32	KAP1	chr6:53659081-53659699	U2OS	brain:	n/a	n/a
33	MAX	chr6:53657848-53661452	HCT-116	colon:	n/a	chr6:53660589-53660599
34	CTCF	chr6:53659190-53659353	GM12891	blood:	n/a	n/a
35	CTCF	chr6:53659100-53659471	H1-hESC	embryonic stem cell:	n/a	n/a
36	TBP	chr6:53658870-53660561	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr6:53659209-53659459	A549	lung:	n/a	n/a
38	CTCF	chr6:53659166-53659400	MCF-7	breast:	n/a	n/a
39	MYC	chr6:53658968-53659867	MCF10A-Er-Src	breast:	n/a	n/a
40	CTCF	chr6:53659100-53659250	HFF	foreskin:	n/a	n/a
41	CTCF	chr6:53659160-53659310	HRPEpiC	eye:	n/a	n/a
42	RAD21	chr6:53658916-53660298	H1-hESC	embryonic stem cell:	n/a	chr6:53659267-53659276
43	TEAD4	chr6:53658886-53659884	HepG2	liver:	n/a	n/a
44	CTCF	chr6:53659200-53659350	Caco-2	colon:	n/a	n/a
45	POLR2A	chr6:53659104-53660007	Hela-S3	cervix:	n/a	n/a
46	CTCF	chr6:53659200-53659350	WERI-Rb-1	eye:	n/a	n/a
47	GABPA	chr6:53658939-53659968	HL-60	blood:	n/a	n/a
48	TBP	chr6:53659116-53659746	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr6:53659175-53659390	MCF-7	breast:	n/a	n/a
50	CTCF	chr6:53659154-53659236	GM20000	blood:	n/a	n/a

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

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

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10456165	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10456673	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10456674	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10948768	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11962552	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11968082	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12202762	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12204130	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12211417	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12211478	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12213577	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12216441	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13205690	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13211528	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17748374	0.82[AFR][1000 genomes]
rs34876933	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35078422	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35143842	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35868455	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35971619	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4373362	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55931905	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72941941	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7762326	0.82[AFR][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
rs34113003	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	chr6:53658000-53659400	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr6:53658000-53660200	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr6:53658000-53660200	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr6:53658000-53660400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:53658000-53660400	Active TSS	Rectal Smooth Muscle	rectum
18	chr6:53658000-53660600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:53658000-53660600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:53658000-53660600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:53658000-53660800	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr6:53658000-53661000	Active TSS	H9 Cell Line	embryonic stem cell
23	chr6:53658000-53661000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:53658000-53661400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:53658000-53661400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:53658000-53661400	Active TSS	Aorta	Aorta
27	chr6:53658000-53661400	Active TSS	Esophagus	oesophagus
28	chr6:53658000-53661600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:53658000-53661600	Active TSS	Fetal Intestine Small	intestine
30	chr6:53658000-53662000	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr6:53658200-53659400	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr6:53658200-53659400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr6:53658200-53659400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr6:53658200-53659400	Flanking Active TSS	Fetal Muscle Leg	muscle
35	chr6:53658200-53659600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
36	chr6:53658200-53659600	Flanking Active TSS	HUVEC	blood vessel
37	chr6:53658200-53660200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:53658200-53660200	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr6:53658200-53660400	Active TSS	Left Ventricle	heart
40	chr6:53658200-53660400	Active TSS	Pancreas	Pancrea
41	chr6:53658200-53660600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr6:53658200-53660800	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr6:53658200-53660800	Active TSS	Right Atrium	heart
44	chr6:53658200-53661000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr6:53658200-53661000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:53658200-53661000	Active TSS	Fetal Heart	heart
47	chr6:53658200-53661200	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr6:53658200-53661400	Active TSS	Brain Substantia Nigra	brain
49	chr6:53658200-53661400	Active TSS	Gastric	stomach
50	chr6:53658200-53661400	Active TSS	Ovary	ovary

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