Variant report

Variant	rs2057727
Chromosome Location	chr6:30297529-30297530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30297025-30297671	HL-60	blood:	n/a	n/a
2	SPI1	chr6:30296979-30297568	HL-60	blood:	n/a	n/a
3	REST	chr6:30296947-30297574	HL-60	blood:	n/a	n/a
4	POLR2A	chr6:30297072-30297659	K562	blood:	n/a	n/a
5	POLR2A	chr6:30297035-30297751	HL-60	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30297500-30297550	NH-A	brain:	n/a
2	chr6:30297500-30297550	BE2_C	brain:	n/a
3	chr6:30297500-30297550	BJ	skin:	n/a
4	chr6:30297500-30297550	A549	lung:	n/a
5	chr6:30297500-30297550	Caco-2	colon:	n/a
6	chr6:30297500-30297550	SK-N-SH_RA	brain:	n/a
7	chr6:30297500-30297550	AoSMC	blood vessel:	n/a
8	chr6:30297500-30297550	NHBE	bronchial:	n/a
9	chr6:30297500-30297550	ECC-1	luminal epithelium:	n/a
10	chr6:30297500-30297550	HepG2	liver:	n/a
11	chr6:30297500-30297550	ProgFib	skin:	n/a
12	chr6:30297500-30297550	HRCEpiC	kidney:	n/a
13	chr6:30297500-30297550	HIPEpiC	eye:	n/a
14	chr6:30297500-30297550	HEEpiC	esophagus:	n/a
15	chr6:30297500-30297550	HAEpiC	amniotic membrane:	n/a
16	chr6:30297500-30297550	GM12892	blood:	n/a
17	chr6:30297500-30297550	Jurkat	blood:	n/a
18	chr6:30297500-30297550	NT2-D1	testis:	n/a
19	chr6:30297500-30297550	IMR90	lung:	fetal
20	chr6:30297500-30297550	HCM	heart:	n/a
21	chr6:30297500-30297550	HMEC	breast:	n/a
22	chr6:30297500-30297550	AG04449	skin:	fetal
23	chr6:30297500-30297550	HUVEC	blood vessel:	n/a
24	chr6:30297500-30297550	ovcar-3	ovarian:	n/a
25	chr6:30297500-30297550	Hela-S3	cervix:	n/a
26	chr6:30297500-30297550	Hepatocyte	liver:	n/a
27	chr6:30297500-30297550	CMK	blood:	n/a
28	chr6:30297500-30297550	PrEC	prostate:	n/a
29	chr6:30297500-30297550	AG04450	lung:	fetal
30	chr6:30297500-30297550	GM06990	blood:	n/a
31	chr6:30297500-30297550	AG10803	skin:	n/a
32	chr6:30297500-30297550	HNPCEpiC	eye:	n/a
33	chr6:30297500-30297550	PANC-1	pancreas:	n/a
34	chr6:30297500-30297550	MCF-7	breast:	n/a
35	chr6:30297500-30297550	K562	blood:	n/a
36	chr6:30297500-30297550	MCF10A-Er-Src	breast:	n/a
37	chr6:30297500-30297550	SK-N-SH	brain:	n/a
38	chr6:30297500-30297550	PFSK-1	brain:	n/a
39	chr6:30297500-30297550	HCF	heart:	n/a
40	chr6:30297500-30297550	AG09309	skin:	n/a
41	chr6:30297500-30297550	GM12891	blood:	n/a
42	chr6:30297500-30297550	AG09319	gingival:	n/a
43	chr6:30297500-30297550	HCT-116	colon:	n/a
44	chr6:30297500-30297550	HCPEpiC	choroid plexus:	n/a
45	chr6:30297500-30297550	NHDF-neo	bronchial:	n/a
46	chr6:30297500-30297550	RPTEC	kidney:	n/a
47	chr6:30297500-30297550	SKMC	muscle:	n/a
48	chr6:30297500-30297550	HEK293	kidney:	embryo
49	chr6:30297500-30297550	HPAEpiC	pulmonary alveolar:	n/a
50	chr6:30297500-30297550	NB4	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30293058..30297784-chr6:30308514..30315279,24	MCF-7	breast:

No data

Variant related genes	Relation type
HCG17	TF binding region
HCG18	TF binding region
HCG17	CpG island
HCG18	CpG island
ENSG00000241370	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1045251	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1060065	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1264616	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473102	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1579218	0.80[ASN][1000 genomes]
rs1579219	0.80[ASN][1000 genomes]
rs2023476	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2023477	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2023478	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2074474	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2097773	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2285798	0.82[ASN][1000 genomes]
rs2394779	0.83[ASN][1000 genomes]
rs2394780	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2516697	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2516699	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516700	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516702	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516704	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516705	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516706	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516707	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516710	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516713	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523737	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2523744	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523745	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523746	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523747	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523748	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523750	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs261943	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs261948	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs261949	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28360021	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28360023	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844752	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844761	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844763	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844765	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2894145	0.81[ASN][1000 genomes]
rs3778624	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778626	0.81[ASN][1000 genomes]
rs6904208	0.81[AFR][1000 genomes]
rs6912239	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912495	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7452694	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7767653	0.81[AFR][1000 genomes]
rs7767817	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9295843	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295844	0.83[ASN][1000 genomes]
rs9357095	0.83[ASN][1000 genomes]
rs9366755	0.82[ASN][1000 genomes]
rs9368628	0.83[ASN][1000 genomes]
rs9368632	0.83[ASN][1000 genomes]
rs9368633	0.83[ASN][1000 genomes]
rs9380168	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380174	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9391679	0.83[ASN][1000 genomes]
rs9391806	0.83[ASN][1000 genomes]
rs9391807	0.83[ASN][1000 genomes]
rs9393999	0.83[ASN][1000 genomes]
rs9394000	0.83[ASN][1000 genomes]
rs9394001	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394002	0.81[ASN][1000 genomes]
rs9394003	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs962899	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs974963	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2057727	LOC401245	cis	multi-tissue	Pritchard
rs2057727	TRIM26	Cis_1M	lymphoblastoid	RTeQTL
rs2057727	HCG18	cis	normal skin	skin_eQTL
rs2057727	HCG18	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30295400-30303400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:30295400-30309400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:30295600-30299400	Weak transcription	Stomach Mucosa	stomach
4	chr6:30295600-30301800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:30295600-30303400	Weak transcription	Psoas Muscle	Psoas
6	chr6:30295600-30312600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:30295600-30312600	Weak transcription	Right Atrium	heart
8	chr6:30295600-30313000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:30295800-30297600	Weak transcription	Primary T cells from cord blood	blood
10	chr6:30295800-30303200	Weak transcription	NHDF-Ad	bronchial
11	chr6:30295800-30303400	Weak transcription	A549	lung
12	chr6:30295800-30311000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:30295800-30312400	Weak transcription	Fetal Heart	heart
14	chr6:30295800-30312400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:30296000-30297600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:30296000-30297600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:30296000-30297800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr6:30296200-30310400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:30296600-30299600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:30296600-30310600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr6:30296800-30298600	Strong transcription	Hela-S3	cervix
22	chr6:30296800-30299200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:30296800-30299600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:30296800-30300400	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:30296800-30301000	Strong transcription	NH-A	brain
26	chr6:30296800-30310000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:30296800-30310000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr6:30296800-30310200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:30296800-30310400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr6:30296800-30310600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:30296800-30310800	Strong transcription	Fetal Brain Female	brain
32	chr6:30296800-30311200	Strong transcription	Placenta	Placenta
33	chr6:30296800-30311400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:30296800-30311800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr6:30297000-30298000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr6:30297000-30299000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:30297000-30299000	Strong transcription	Fetal Intestine Small	intestine
38	chr6:30297000-30299400	Strong transcription	Fetal Stomach	stomach
39	chr6:30297000-30299400	Strong transcription	Lung	lung
40	chr6:30297000-30299600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:30297000-30299600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:30297000-30299800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:30297000-30299800	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr6:30297000-30300000	Strong transcription	Brain Hippocampus Middle	brain
45	chr6:30297000-30300200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:30297000-30300200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:30297000-30300200	Strong transcription	Fetal Muscle Leg	muscle
48	chr6:30297000-30300400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr6:30297000-30300400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr6:30297000-30300400	Strong transcription	Fetal Muscle Trunk	muscle

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