Variant report

Variant	rs73576330
Chromosome Location	chr6:142623153-142623154
allele	G/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	POLR2A	chr6:142622738-142623649	ProgFib	skin:	n/a	n/a
2	MAZ	chr6:142622961-142623451	Hela-S3	cervix:	n/a	n/a
3	SMARCC1	chr6:142621664-142623934	Hela-S3	cervix:	n/a	n/a
4	ARID3A	chr6:142622792-142623208	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:142621261-142624876	PANC-1	pancreas:	n/a	n/a
6	TCF12	chr6:142622284-142623358	ECC-1	luminal epithelium:	n/a	chr6:142622887-142622897 chr6:142622665-142622675 chr6:142622979-142622986
7	RAD21	chr6:142622802-142623253	MCF-7	breast:	n/a	chr6:142622982-142622995
8	ZNF263	chr6:142622593-142623592	HEK293-T-REx	kidney:	n/a	n/a
9	CTCF	chr6:142623020-142623170	NHEK	skin:	n/a	chr6:142623096-142623109 chr6:142623100-142623113
10	SIN3AK20	chr6:142622664-142624089	MCF-7	breast:	n/a	n/a
11	FOXA1	chr6:142622823-142624139	HepG2	liver:	n/a	n/a
12	HNF4G	chr6:142622828-142623392	HepG2	liver:	n/a	n/a
13	POLR2A	chr6:142621379-142624744	HUVEC	blood vessel:	n/a	n/a
14	CEBPD	chr6:142622710-142623479	HepG2	liver:	n/a	n/a
15	CTCF	chr6:142622860-142623356	H1-hESC	embryonic stem cell:	n/a	chr6:142623096-142623109 chr6:142623100-142623113
16	YY1	chr6:142622858-142623391	ECC-1	luminal epithelium:	n/a	chr6:142622966-142622980 chr6:142623099-142623113 chr6:142623005-142623019
17	EGR1	chr6:142622768-142623485	MCF-7	breast:	n/a	chr6:142623106-142623116 chr6:142623103-142623116 chr6:142623106-142623115
18	POLR2A	chr6:142622621-142623416	Hela-S3	cervix:	n/a	n/a
19	FOXA2	chr6:142623089-142623966	A549	lung:	n/a	n/a
20	MAZ	chr6:142622897-142623279	HepG2	liver:	n/a	n/a
21	POLR2A	chr6:142622492-142623951	MCF-7	breast:	n/a	n/a
22	NFIC	chr6:142622676-142624210	HepG2	liver:	n/a	chr6:142623640-142623656 chr6:142623639-142623656
23	MAX	chr6:142622851-142623847	SK-N-SH	brain:	n/a	n/a
24	ZBTB7A	chr6:142622400-142623570	ECC-1	luminal epithelium:	n/a	n/a
25	ELK1	chr6:142622969-142623210	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr6:142621686-142623227	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr6:142622790-142623404	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr6:142621656-142624313	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr6:142621895-142623437	HUVEC	blood vessel:	n/a	n/a
30	RCOR1	chr6:142622849-142623278	Hela-S3	cervix:	n/a	n/a
31	YY1	chr6:142623119-142623296	A549	lung:	n/a	n/a
32	E2F6	chr6:142622787-142623766	A549	lung:	n/a	n/a
33	CTCF	chr6:142622954-142623186	A549	lung:	n/a	chr6:142623096-142623109 chr6:142623100-142623113
34	PML	chr6:142622783-142623447	MCF-7	breast:	n/a	n/a
35	HDAC2	chr6:142622748-142623542	HepG2	liver:	n/a	n/a
36	POLR2A	chr6:142621685-142623763	HUVEC	blood vessel:	n/a	n/a
37	BHLHE40	chr6:142622886-142623212	HepG2	liver:	n/a	n/a
38	TCF12	chr6:142622803-142624114	A549	lung:	n/a	chr6:142622887-142622897 chr6:142622979-142622986
39	CTCF	chr6:142623040-142623190	HRE	kidney:	n/a	chr6:142623096-142623109 chr6:142623100-142623113
40	MAX	chr6:142621679-142624627	HepG2	liver:	n/a	chr6:142622591-142622601
41	TBP	chr6:142622659-142623461	H1-hESC	embryonic stem cell:	n/a	n/a
42	MBD4	chr6:142622640-142624781	HepG2	liver:	n/a	n/a
43	KAP1	chr6:142622800-142623405	HEK293	kidney:	n/a	n/a
44	YY1	chr6:142622477-142623504	HepG2	liver:	n/a	chr6:142622966-142622980 chr6:142623099-142623113 chr6:142623005-142623019
45	MAX	chr6:142621741-142624053	HCT-116	colon:	n/a	chr6:142622591-142622601
46	HA-E2F1	chr6:142622109-142624108	MCF-7	breast:	n/a	n/a
47	POLR2A	chr6:142622797-142623465	Gliobla	brain:	n/a	n/a
48	BACH1	chr6:142623058-142623526	H1-hESC	embryonic stem cell:	n/a	n/a
49	FOXA2	chr6:142621749-142624322	HepG2	liver:	n/a	n/a
50	CTCF	chr6:142623060-142623210	AG04450	lung:	n/a	chr6:142623096-142623109 chr6:142623100-142623113

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:142622193..142623879-chr6:143265828..143267526,2	MCF-7	breast:
2	chr5:43121611..43122180-chr6:142622739..142623312,2	Hela-S3	cervix:

Variant related genes	Relation type
GPR126	TF binding region
ENSG00000172262	Chromatin interaction
ENSG00000010818	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs57244265	1.00[AMR][1000 genomes]
rs59260394	1.00[AMR][1000 genomes]
rs59280767	0.92[AMR][1000 genomes]
rs59648555	1.00[AMR][1000 genomes]
rs60258191	1.00[AMR][1000 genomes]
rs61299002	0.84[AMR][1000 genomes]
rs6905012	1.00[AMR][1000 genomes]
rs6906368	1.00[AMR][1000 genomes]
rs6906539	1.00[AMR][1000 genomes]
rs6920468	0.92[AMR][1000 genomes]
rs6920602	0.92[AMR][1000 genomes]
rs6926685	1.00[AMR][1000 genomes]
rs73576305	1.00[AMR][1000 genomes]
rs73576312	1.00[AMR][1000 genomes]
rs73576315	1.00[AMR][1000 genomes]
rs73576325	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73576327	0.82[AFR][1000 genomes];1.00[AMR][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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1029666	chr6:142594099-142643084	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv275340	chr6:142620405-142624568	Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142621800-142625600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:142622000-142623200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:142622000-142623400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:142622000-142623400	Enhancers	Spleen	Spleen
5	chr6:142622000-142623600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
6	chr6:142622000-142623800	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr6:142622000-142624000	Active TSS	Fetal Kidney	kidney
8	chr6:142622000-142624200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr6:142622000-142624600	Active TSS	Rectal Smooth Muscle	rectum
10	chr6:142622200-142623200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:142622200-142623200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:142622200-142623200	Active TSS	Brain Anterior Caudate	brain
13	chr6:142622200-142623400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:142622200-142623400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:142622200-142623400	Active TSS	Primary T cells from cord blood	blood
16	chr6:142622200-142623400	Active TSS	Fetal Intestine Small	intestine
17	chr6:142622200-142623400	Active TSS	Pancreas	Pancrea
18	chr6:142622200-142623400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
19	chr6:142622200-142623400	Bivalent/Poised TSS	Small Intestine	intestine
20	chr6:142622200-142623400	Active TSS	NHDF-Ad	bronchial
21	chr6:142622200-142623600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr6:142622200-142623600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
23	chr6:142622200-142623600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr6:142622200-142623600	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr6:142622200-142623600	Active TSS	HSMMtube	muscle
26	chr6:142622200-142623800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:142622200-142623800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
28	chr6:142622200-142623800	Active TSS	Colonic Mucosa	Colon
29	chr6:142622200-142623800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
30	chr6:142622200-142624200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
31	chr6:142622200-142624200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
32	chr6:142622200-142624200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
33	chr6:142622200-142624600	Active TSS	Esophagus	oesophagus
34	chr6:142622200-142624600	Active TSS	Placenta Amnion	Placenta Amnion
35	chr6:142622200-142624800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
36	chr6:142622200-142625000	Bivalent/Poised TSS	HepG2	liver
37	chr6:142622200-142626400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:142622200-142626800	Active TSS	A549	lung
39	chr6:142622400-142623200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:142622400-142623200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:142622400-142623200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:142622400-142623200	Active TSS	Fetal Intestine Large	intestine
43	chr6:142622400-142623400	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr6:142622400-142623400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr6:142622400-142623400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
46	chr6:142622400-142623400	Bivalent Enhancer	Fetal Brain Male	brain
47	chr6:142622400-142623600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:142622400-142623600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:142622400-142623600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr6:142622400-142623600	Bivalent/Poised TSS	Brain Substantia Nigra	brain

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