Variant report

Variant	rs17187658
Chromosome Location	chr6:30029343-30029344
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:273)
CpG islands
(count:61)
Chromatin interactive
region (count:16)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:273 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFYA	chr6:30028576-30029359	Hela-S3	cervix:	n/a	n/a
2	MAX	chr6:30028324-30030090	MCF-7	breast:	n/a	n/a
3	CBX3	chr6:30029329-30030139	K562	blood:	n/a	n/a
4	TEAD4	chr6:30028437-30029462	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:30028331-30029541	Raji	blood:	n/a	n/a
6	POLR2A	chr6:30028318-30029641	K562	blood:	n/a	n/a
7	TBL1XR1	chr6:30028484-30029474	K562	blood:	n/a	n/a
8	MYC	chr6:30028358-30029428	K562	blood:	n/a	n/a
9	NFIC	chr6:30028650-30029421	HepG2	liver:	n/a	n/a
10	MAX	chr6:30028442-30029648	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr6:30028676-30029824	GM12878	blood:	n/a	n/a
12	PML	chr6:30028399-30029917	GM12878	blood:	n/a	n/a
13	YY1	chr6:30029274-30029877	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:30028555-30029405	U87	brain:	n/a	n/a
15	POLR2A	chr6:30028203-30030091	HepG2	liver:	n/a	n/a
16	SRF	chr6:30028541-30029452	HCT-116	colon:	n/a	n/a
17	POLR2A	chr6:30028288-30029795	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr6:30028658-30029465	A549	lung:	n/a	n/a
19	MYC	chr6:30028407-30029470	MCF10A-Er-Src	breast:	n/a	n/a
20	TAF1	chr6:30028642-30029790	PFSK-1	brain:	n/a	n/a
21	TCF7L2	chr6:30028784-30029632	Hela-S3	cervix:	n/a	n/a
22	BHLHE40	chr6:30028769-30029459	HepG2	liver:	n/a	n/a
23	MAFK	chr6:30028377-30030142	K562	blood:	n/a	n/a
24	POLR2A	chr6:30028627-30029426	SK-N-MC	brain:	n/a	n/a
25	REST	chr6:30028655-30029427	HepG2	liver:	n/a	n/a
26	POLR2A	chr6:30028273-30029658	H1-neurons	neurons:	n/a	n/a
27	MBD4	chr6:30028291-30030076	HepG2	liver:	n/a	n/a
28	RELA	chr6:30028611-30029470	GM12892	blood:	n/a	n/a
29	TAF1	chr6:30028220-30029901	K562	blood:	n/a	n/a
30	TCF12	chr6:30028637-30029378	ECC-1	luminal epithelium:	n/a	n/a
31	MYC	chr6:30027984-30029471	A549	lung:	n/a	n/a
32	POLR2A	chr6:30028350-30029420	HUVEC	blood vessel:	n/a	n/a
33	MXI1	chr6:30028113-30030563	SK-N-SH	brain:	n/a	n/a
34	IRF1	chr6:30028729-30029445	K562	blood:	n/a	n/a
35	SIN3A	chr6:30028658-30029833	GM12878	blood:	n/a	n/a
36	POLR2A	chr6:30028124-30030211	K562	blood:	n/a	n/a
37	POLR2A	chr6:30028445-30029730	GM18951	blood:	n/a	n/a
38	TFAP2A	chr6:30028701-30029391	Hela-S3	cervix:	n/a	n/a
39	HEY1	chr6:30028407-30029843	HepG2	liver:	n/a	n/a
40	CHD2	chr6:30028804-30029357	HepG2	liver:	n/a	n/a
41	HEY1	chr6:30028341-30029361	K562	blood:	n/a	n/a
42	POLR2A	chr6:30028222-30029922	K562	blood:	n/a	n/a
43	MYBL2	chr6:30028375-30029783	HepG2	liver:	n/a	n/a
44	BRCA1	chr6:30028723-30029609	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr6:30028425-30029745	GM19193	blood:	n/a	n/a
46	NFIC	chr6:30028457-30029379	GM12878	blood:	n/a	n/a
47	EP300	chr6:30028706-30029498	HepG2	liver:	n/a	n/a
48	HDAC2	chr6:30028781-30029480	HepG2	liver:	n/a	n/a
49	HNF4G	chr6:30028742-30029590	HepG2	liver:	n/a	n/a
50	POLR2A	chr6:30028461-30029667	MCF-7	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30029319-30029369	H1-hESC	embryonic stem cell:	embryo
2	chr6:30029319-30029369	Caco-2	colon:	n/a
3	chr6:30029319-30029369	Hela-S3	cervix:	n/a
4	chr6:30029319-30029369	SK-N-SH	brain:	n/a
5	chr6:30029319-30029369	Jurkat	blood:	n/a
6	chr6:30029319-30029369	T-47D	breast:	n/a
7	chr6:30029319-30029369	HMEC	breast:	n/a
8	chr6:30029319-30029369	HPAEpiC	pulmonary alveolar:	n/a
9	chr6:30029319-30029369	PrEC	prostate:	n/a
10	chr6:30029319-30029369	NB4	blood:	n/a
11	chr6:30029319-30029369	HAEpiC	amniotic membrane:	n/a
12	chr6:30029319-30029369	A549	lung:	n/a
13	chr6:30029319-30029369	SAEC	small airway:	n/a
14	chr6:30029319-30029369	HCM	heart:	n/a
15	chr6:30029319-30029369	ProgFib	skin:	n/a
16	chr6:30029319-30029369	NHBE	bronchial:	n/a
17	chr6:30029319-30029369	GM12892	blood:	n/a
18	chr6:30029319-30029369	HRCEpiC	kidney:	n/a
19	chr6:30029319-30029369	HEEpiC	esophagus:	n/a
20	chr6:30029319-30029369	SK-N-MC	brain:	n/a
21	chr6:30029319-30029369	GM12891	blood:	n/a
22	chr6:30029319-30029369	LNCaP	prostate:	n/a
23	chr6:30029319-30029369	AoSMC	blood vessel:	n/a
24	chr6:30029319-30029369	HCF	heart:	n/a
25	chr6:30029319-30029369	HRPEpiC	eye:	n/a
26	chr6:30029319-30029369	HNPCEpiC	eye:	n/a
27	chr6:30029319-30029369	HUVEC	blood vessel:	n/a
28	chr6:30029319-30029369	AG04450	lung:	fetal
29	chr6:30029319-30029369	AG09319	gingival:	n/a
30	chr6:30029319-30029369	HepG2	liver:	n/a
31	chr6:30029319-30029369	AG09309	skin:	n/a
32	chr6:30029319-30029369	PANC-1	pancreas:	n/a
33	chr6:30029319-30029369	HCT-116	colon:	n/a
34	chr6:30029319-30029369	ECC-1	luminal epithelium:	n/a
35	chr6:30029319-30029369	PFSK-1	brain:	n/a
36	chr6:30029319-30029369	HCPEpiC	choroid plexus:	n/a
37	chr6:30029319-30029369	IMR90	lung:	fetal
38	chr6:30029319-30029369	MCF10A-Er-Src	breast:	n/a
39	chr6:30029319-30029369	NT2-D1	testis:	n/a
40	chr6:30029319-30029369	RPTEC	kidney:	n/a
41	chr6:30029319-30029369	AG10803	skin:	n/a
42	chr6:30029319-30029369	MCF-7	breast:	n/a
43	chr6:30029319-30029369	HEK293	kidney:	embryo
44	chr6:30029319-30029369	NHDF-neo	bronchial:	n/a
45	chr6:30029319-30029369	ovcar-3	ovarian:	n/a
46	chr6:30029319-30029369	SKMC	muscle:	n/a
47	chr6:30029319-30029369	HL-60	blood:	n/a
48	chr6:30029319-30029369	HIPEpiC	eye:	n/a
49	chr6:30029319-30029369	K562	blood:	n/a
50	chr6:30029319-30029369	GM12878	blood:	n/a

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30028084..30030840-chr6:30103303..30105686,3	MCF-7	breast:
2	chr19:39897352..39897996-chr6:30028513..30029383,2	Hela-S3	cervix:
3	chr17:34136416..34136960-chr6:30028632..30029577,2	Hela-S3	cervix:
4	chr6:30002740..30005205-chr6:30029200..30030838,2	MCF-7	breast:
5	chr6:30028230..30030474-chr6:30075345..30077234,2	MCF-7	breast:
6	chr6:30027015..30030813-chr6:30040823..30045193,4	K562	blood:
7	chr1:198126044..198126586-chr6:30028621..30029511,2	Hela-S3	cervix:
8	chr17:59475970..59478357-chr6:30028344..30030119,2	MCF-7	breast:
9	chr6:30028283..30029937-chr6:30312414..30314218,2	K562	blood:
10	chr2:96873467..96874218-chr6:30028960..30029487,2	Hela-S3	cervix:
11	chr17:7387553..7388054-chr6:30029263..30029975,2	Hela-S3	cervix:
12	chr6:30002424..30006428-chr6:30027567..30030890,5	MCF-7	breast:
13	chr15:90931536..90932447-chr6:30029025..30029813,2	Hela-S3	cervix:
14	chr6:30028283..30030226-chr6:30312404..30313914,2	K562	blood:
15	chr6:30029044..30029552-chr8:11659926..11660449,2	HCT-116	colon:
16	chr4:144264296..144264969-chr6:30028972..30029813,2	Hela-S3	cervix:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF39-4	chr6:30028518-30029417	ENSG00000204623

No data

Variant related genes	Relation type
ZNRD1-AS1	TF binding region
ZNRD1-AS1	CpG island
ENSG00000267280	Chromatin interaction
ENSG00000265623	Chromatin interaction
ENSG00000151414	Chromatin interaction
ENSG00000172660	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000241370	Chromatin interaction
ENSG00000079459	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000140575	Chromatin interaction
ENSG00000204618	Chromatin interaction
ENSG00000204616	Chromatin interaction
ENSG00000255046	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000204614	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs17180528	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17186951	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17187553	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17187826	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17187847	1.00[EUR][1000 genomes]
rs17194258	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3888631	1.00[ASN][1000 genomes]
rs4713289	1.00[EUR][1000 genomes]
rs4959042	1.00[EUR][1000 genomes]
rs55945512	1.00[ASN][1000 genomes]
rs56908820	1.00[EUR][1000 genomes]
rs57303436	1.00[ASN][1000 genomes]
rs59812435	1.00[ASN][1000 genomes]
rs6917420	1.00[EUR][1000 genomes]
rs73725925	1.00[ASN][1000 genomes]
rs73725942	1.00[ASN][1000 genomes]
rs73725957	1.00[ASN][1000 genomes]
rs73725968	1.00[ASN][1000 genomes]
rs73727658	1.00[ASN][1000 genomes]
rs7740741	1.00[EUR][1000 genomes]

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	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30027600-30030200	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr6:30027600-30031000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:30027800-30029400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:30027800-30029600	Active TSS	Right Atrium	heart
5	chr6:30027800-30029800	Active TSS	H9 Cell Line	embryonic stem cell
6	chr6:30027800-30029800	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr6:30027800-30029800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:30027800-30029800	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:30027800-30030000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:30027800-30030000	Active TSS	Aorta	Aorta
11	chr6:30027800-30030200	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr6:30027800-30030200	Active TSS	Esophagus	oesophagus
13	chr6:30028000-30029600	Active TSS	Brain Anterior Caudate	brain
14	chr6:30028000-30029800	Active TSS	H1 Cell Line	embryonic stem cell
15	chr6:30028000-30029800	Active TSS	Fetal Kidney	kidney
16	chr6:30028000-30029800	Active TSS	Fetal Muscle Trunk	muscle
17	chr6:30028000-30029800	Active TSS	Right Ventricle	heart
18	chr6:30028000-30030000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:30028000-30030000	Active TSS	Ovary	ovary
20	chr6:30028000-30030000	Active TSS	A549	lung
21	chr6:30028000-30030000	Bivalent/Poised TSS	HepG2	liver
22	chr6:30028000-30030200	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr6:30028000-30030200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:30028000-30030200	Active TSS	Psoas Muscle	Psoas
25	chr6:30028200-30029400	Active TSS	Colonic Mucosa	Colon
26	chr6:30028200-30029600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:30028200-30029600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:30028200-30029600	Active TSS	Brain Angular Gyrus	brain
29	chr6:30028200-30029600	Active TSS	Brain Hippocampus Middle	brain
30	chr6:30028200-30029600	ZNF genes & repeats	Fetal Brain Male	brain
31	chr6:30028200-30029600	Active TSS	Placenta Amnion	Placenta Amnion
32	chr6:30028200-30029800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:30028200-30029800	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr6:30028200-30029800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:30028200-30029800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:30028200-30029800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:30028200-30029800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:30028200-30029800	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr6:30028200-30029800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:30028200-30029800	Active TSS	Muscle Satellite Cultured Cells	--
41	chr6:30028200-30029800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:30028200-30029800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:30028200-30029800	Active TSS	Left Ventricle	heart
44	chr6:30028200-30029800	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr6:30028200-30029800	Active TSS	HMEC	breast
46	chr6:30028200-30029800	Active TSS	NHDF-Ad	bronchial
47	chr6:30028200-30029800	Active TSS	NHEK	skin
48	chr6:30028200-30030000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr6:30028200-30030000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr6:30028200-30030000	Active TSS	Fetal Intestine Small	intestine

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