Variant report

Variant	rs6776157
Chromosome Location	chr3:156543482-156543483
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:152)
CpG islands
(count:61)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:152 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr3:156543234-156543577	HCT-116	colon:	n/a	n/a
2	POLR2A	chr3:156543159-156545423	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:156543327-156544811	HUVEC	blood vessel:	n/a	n/a
4	JUN	chr3:156543232-156543548	K562	blood:	n/a	n/a
5	POLR2A	chr3:156543209-156543697	K562	blood:	n/a	n/a
6	POLR2A	chr3:156543217-156545003	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr3:156543056-156544874	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:156543240-156544979	Hela-S3	cervix:	n/a	n/a
9	ZKSCAN1	chr3:156543239-156544897	Hela-S3	cervix:	n/a	n/a
10	MAX	chr3:156543304-156544834	K562	blood:	n/a	chr3:156544061-156544070
11	HEY1	chr3:156543199-156544879	K562	blood:	n/a	n/a
12	POLR2A	chr3:156542971-156545221	Hela-S3	cervix:	n/a	n/a
13	MAX	chr3:156543225-156545079	A549	lung:	n/a	chr3:156544061-156544070
14	POLR2A	chr3:156543240-156544926	GM12878	blood:	n/a	n/a
15	RAD21	chr3:156543340-156544900	Hela-S3	cervix:	n/a	n/a
16	FOSL1	chr3:156543216-156543513	K562	blood:	n/a	chr3:156543379-156543390
17	MAX	chr3:156543378-156544852	MCF-7	breast:	n/a	chr3:156544061-156544070
18	POLR2A	chr3:156543263-156544968	K562	blood:	n/a	n/a
19	CBX3	chr3:156543137-156544892	K562	blood:	n/a	n/a
20	MAX	chr3:156543352-156544688	NB4	blood:	n/a	chr3:156544061-156544070
21	E2F6	chr3:156543323-156544810	K562	blood:	n/a	chr3:156544104-156544113
22	PML	chr3:156543263-156544981	GM12878	blood:	n/a	n/a
23	EP300	chr3:156543312-156545124	GM12878	blood:	n/a	n/a
24	RCOR1	chr3:156543281-156544999	K562	blood:	n/a	n/a
25	POLR2A	chr3:156543232-156544902	GM12891	blood:	n/a	n/a
26	TBL1XR1	chr3:156543429-156544772	K562	blood:	n/a	n/a
27	MXI1	chr3:156543381-156544988	GM12878	blood:	n/a	n/a
28	SMC3	chr3:156543273-156545193	Hela-S3	cervix:	n/a	n/a
29	ARID3A	chr3:156543256-156544114	K562	blood:	n/a	n/a
30	TCF7L2	chr3:156543396-156544851	HCT-116	colon:	n/a	chr3:156543512-156543521
31	REST	chr3:156543180-156545046	A549	lung:	n/a	chr3:156543867-156543876 chr3:156543863-156543876
32	POLR2A	chr3:156543245-156545450	A549	lung:	n/a	n/a
33	POLR2A	chr3:156543282-156544924	HL-60	blood:	n/a	n/a
34	MAX	chr3:156543207-156545213	MCF-7	breast:	n/a	chr3:156544061-156544070
35	MXI1	chr3:156543044-156545306	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr3:156543295-156544896	ProgFib	skin:	n/a	n/a
37	MAX	chr3:156543000-156545045	HCT-116	colon:	n/a	chr3:156544061-156544070
38	FOS	chr3:156543259-156543551	MCF10A-Er-Src	breast:	n/a	n/a
39	RAD21	chr3:156543152-156545042	IMR90	lung:	n/a	n/a
40	HEY1	chr3:156543320-156544809	K562	blood:	n/a	n/a
41	GABPA	chr3:156543292-156544920	MCF-7	breast:	n/a	n/a
42	POLR2A	chr3:156543264-156544920	GM19099	blood:	n/a	n/a
43	IRF1	chr3:156543454-156544672	K562	blood:	n/a	chr3:156543681-156543694
44	MTA3	chr3:156543110-156545022	GM12878	blood:	n/a	n/a
45	JUN	chr3:156543063-156546460	K562	blood:	n/a	n/a
46	MAZ	chr3:156543163-156545406	IMR90	lung:	n/a	chr3:156544061-156544070
47	SP1	chr3:156542867-156545127	HCT-116	colon:	n/a	n/a
48	POLR2A	chr3:156542970-156544935	HCT-116	colon:	n/a	n/a
49	ATF3	chr3:156543197-156543535	K562	blood:	n/a	n/a
50	ZMIZ1	chr3:156543230-156543485	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:156543471-156543521	NHDF-neo	bronchial:	n/a
2	chr3:156543471-156543521	PrEC	prostate:	n/a
3	chr3:156543471-156543521	BE2_C	brain:	n/a
4	chr3:156543471-156543521	NHBE	bronchial:	n/a
5	chr3:156543471-156543521	HL-60	blood:	n/a
6	chr3:156543471-156543521	Hela-S3	cervix:	n/a
7	chr3:156543471-156543521	HPAEpiC	pulmonary alveolar:	n/a
8	chr3:156543471-156543521	NT2-D1	testis:	n/a
9	chr3:156543471-156543521	SK-N-MC	brain:	n/a
10	chr3:156543471-156543521	GM19239	blood:	n/a
11	chr3:156543471-156543521	NH-A	brain:	n/a
12	chr3:156543471-156543521	U87	brain:	n/a
13	chr3:156543471-156543521	BJ	skin:	n/a
14	chr3:156543471-156543521	ECC-1	luminal epithelium:	n/a
15	chr3:156543471-156543521	SAEC	small airway:	n/a
16	chr3:156543471-156543521	PANC-1	pancreas:	n/a
17	chr3:156543471-156543521	Hepatocyte	liver:	n/a
18	chr3:156543471-156543521	HEEpiC	esophagus:	n/a
19	chr3:156543471-156543521	HRE	kidney:	n/a
20	chr3:156543471-156543521	GM06990	blood:	n/a
21	chr3:156543471-156543521	Jurkat	blood:	n/a
22	chr3:156543471-156543521	AG04449	skin:	fetal
23	chr3:156543471-156543521	HMEC	breast:	n/a
24	chr3:156543471-156543521	Caco-2	colon:	n/a
25	chr3:156543471-156543521	IMR90	lung:	fetal
26	chr3:156543471-156543521	HCPEpiC	choroid plexus:	n/a
27	chr3:156543471-156543521	PFSK-1	brain:	n/a
28	chr3:156543471-156543521	CMK	blood:	n/a
29	chr3:156543471-156543521	HRCEpiC	kidney:	n/a
30	chr3:156543471-156543521	A549	lung:	n/a
31	chr3:156543471-156543521	HCT-116	colon:	n/a
32	chr3:156543471-156543521	LNCaP	prostate:	n/a
33	chr3:156543471-156543521	MCF10A-Er-Src	breast:	n/a
34	chr3:156543471-156543521	HepG2	liver:	n/a
35	chr3:156543471-156543521	GM12892	blood:	n/a
36	chr3:156543471-156543521	SK-N-SH	brain:	n/a
37	chr3:156543471-156543521	HNPCEpiC	eye:	n/a
38	chr3:156543471-156543521	HEK293	kidney:	embryo
39	chr3:156543471-156543521	T-47D	breast:	n/a
40	chr3:156543471-156543521	AG09319	gingival:	n/a
41	chr3:156543471-156543521	HAEpiC	amniotic membrane:	n/a
42	chr3:156543471-156543521	SK-N-SH_RA	brain:	n/a
43	chr3:156543471-156543521	HIPEpiC	eye:	n/a
44	chr3:156543471-156543521	ovcar-3	ovarian:	n/a
45	chr3:156543471-156543521	GM12891	blood:	n/a
46	chr3:156543471-156543521	NB4	blood:	n/a
47	chr3:156543471-156543521	SKMC	muscle:	n/a
48	chr3:156543471-156543521	AoSMC	blood vessel:	n/a
49	chr3:156543471-156543521	HCM	heart:	n/a
50	chr3:156543471-156543521	HRPEpiC	eye:	n/a

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:156542707..156546513-chr3:156875626..156880471,4	K562	blood:
2	chr3:156398881..156401137-chr3:156542792..156545641,2	MCF-7	breast:
3	chr3:156268894..156273100-chr3:156541711..156545313,4	MCF-7	breast:
4	chr3:156543166..156544685-chr3:156806392..156807926,2	K562	blood:
5	chr3:156390293..156396385-chr3:156542364..156548172,18	MCF-7	breast:
6	chr3:156527949..156530289-chr3:156543460..156546861,3	K562	blood:
7	chr3:156390535..156395368-chr3:156542467..156546251,7	MCF-7	breast:
8	chr3:156527592..156531932-chr3:156540848..156546879,8	MCF-7	breast:
9	chr3:156398799..156400378-chr3:156543351..156545988,2	MCF-7	breast:
10	chr3:156543119..156543620-chr9:130213243..130213882,2	Hela-S3	cervix:
11	chr3:156542698..156545519-chr3:156890354..156893395,4	K562	blood:
12	chr17:7123187..7124006-chr3:156543455..156544032,2	Hela-S3	cervix:
13	chr3:156391796..156394617-chr3:156542307..156544876,4	K562	blood:
14	chr3:156543311..156544068-chr9:34329475..34330005,2	Hela-S3	cervix:
15	chr14:103988216..103989188-chr3:156543435..156544222,2	HCT-116	colon:

No data

Variant related genes	Relation type
LEKR1	TF binding region
LEKR1	CpG island
ENSG00000241135	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000222675	Chromatin interaction
ENSG00000230457	Chromatin interaction
ENSG00000072778	Chromatin interaction
ENSG00000148356	Chromatin interaction
ENSG00000114850	Chromatin interaction
ENSG00000164978	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000243176	Chromatin interaction
ENSG00000197958	Chromatin interaction
ENSG00000166165	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10936037	0.85[ASN][1000 genomes]
rs10936038	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11707914	0.81[AMR][1000 genomes]
rs11711674	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11717133	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12492804	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12497539	0.85[CEU][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13072896	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13086516	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13097325	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1430410	0.88[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1430411	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1560415	0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1560416	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1835372	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2653817	0.83[YRI][hapmap]
rs344071	0.81[YRI][hapmap]
rs344072	0.81[YRI][hapmap]
rs344074	0.80[YRI][hapmap]
rs4680305	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59717073	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7641929	0.85[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9812169	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9820830	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9837271	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9842198	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9858861	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874866	0.85[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6776157	LINC00886	cis	Stomach	GTEx
rs6776157	LINC00886	cis	Esophagus Muscularis	GTEx
rs6776157	LINC00886	cis	Muscle Skeletal	GTEx
rs6776157	LINC00886	cis	lung	GTEx
rs6776157	LINC00886	cis	Artery Tibial	GTEx
rs6776157	LINC00886	cis	Artery Aorta	GTEx
rs6776157	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs6776157	LINC00886	cis	Adipose Subcutaneous	GTEx
rs6776157	LINC00886	cis	Nerve Tibial	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156537000-156543600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:156537000-156543600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:156541800-156543600	Enhancers	Fetal Intestine Small	intestine
4	chr3:156541800-156543800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:156542400-156543600	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr3:156542800-156543600	Weak transcription	Stomach Mucosa	stomach
7	chr3:156543000-156545400	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr3:156543200-156543600	Enhancers	Primary B cells from peripheral blood	blood
9	chr3:156543200-156543600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:156543200-156543600	Flanking Active TSS	Thymus	Thymus
11	chr3:156543200-156543600	Enhancers	HMEC	breast
12	chr3:156543200-156543800	Flanking Active TSS	Fetal Kidney	kidney
13	chr3:156543200-156543800	Flanking Active TSS	Hela-S3	cervix
14	chr3:156543200-156544000	Flanking Active TSS	GM12878-XiMat	blood
15	chr3:156543200-156544000	Flanking Active TSS	K562	blood
16	chr3:156543200-156544600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:156543200-156544800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr3:156543200-156545000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:156543200-156545200	Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr3:156543200-156545200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:156543200-156545200	Flanking Active TSS	HUVEC	blood vessel
22	chr3:156543200-156545400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:156543400-156543600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:156543400-156543600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:156543400-156543600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:156543400-156543600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr3:156543400-156543600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:156543400-156543600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:156543400-156543600	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr3:156543400-156543600	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr3:156543400-156543600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
32	chr3:156543400-156543600	Enhancers	Primary hematopoietic stem cells	blood
33	chr3:156543400-156543600	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr3:156543400-156543600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:156543400-156543600	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr3:156543400-156543600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:156543400-156543600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:156543400-156543600	Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr3:156543400-156543600	Flanking Active TSS	Liver	Liver
40	chr3:156543400-156543600	Flanking Active TSS	Brain Anterior Caudate	brain
41	chr3:156543400-156543600	Flanking Active TSS	Brain Hippocampus Middle	brain
42	chr3:156543400-156543600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr3:156543400-156543600	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr3:156543400-156543600	Enhancers	Esophagus	oesophagus
45	chr3:156543400-156543600	Active TSS	Fetal Brain Female	brain
46	chr3:156543400-156543600	Active TSS	Fetal Lung	lung
47	chr3:156543400-156543600	Enhancers	Placenta	Placenta
48	chr3:156543400-156543600	Enhancers	Fetal Stomach	stomach
49	chr3:156543400-156543600	Enhancers	Pancreas	Pancrea
50	chr3:156543400-156543600	Flanking Active TSS	Right Ventricle	heart

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