Variant report

Variant	rs13219845
Chromosome Location	chr6:33587065-33587066
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HDAC2	chr6:33587003-33587250	K562	blood:	n/a	n/a
2	SMARCC1	chr6:33586961-33588673	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr6:33587060-33587210	HPF	lung:	n/a	n/a
4	CTCF	chr6:33587060-33587210	GM12872	blood:	n/a	n/a
5	CTCF	chr6:33587060-33587210	MCF-7	breast:	n/a	n/a
6	CTCF	chr6:33587020-33587170	A549	lung:	n/a	n/a
7	CTCF	chr6:33587020-33587170	HCT-116	colon:	n/a	n/a
8	MAX	chr6:33586784-33587256	K562	blood:	n/a	n/a
9	CTCF	chr6:33586980-33587130	GM12872	blood:	n/a	n/a
10	CTCF	chr6:33587020-33587170	AoAF	blood vessel:	n/a	n/a
11	RCOR1	chr6:33587050-33587163	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr6:33587020-33587170	AG10803	skin:	n/a	n/a
13	CTCF	chr6:33587060-33587210	K562	blood:	n/a	n/a
14	CTCF	chr6:33587060-33587210	SAEC	small airway:	n/a	n/a
15	CTCF	chr6:33587040-33587190	AoAF	blood vessel:	n/a	n/a
16	CTCF	chr6:33587060-33587210	WERI-Rb-1	eye:	n/a	n/a
17	CTCF	chr6:33587053-33587222	MCF-7	breast:	n/a	n/a
18	CTCF	chr6:33587060-33587210	HepG2	liver:	n/a	n/a
19	CTCF	chr6:33587040-33587190	HEK293	kidney:	n/a	n/a
20	CTCF	chr6:33586920-33587070	GM12869	blood:	n/a	n/a
21	SMC3	chr6:33587033-33587411	Hela-S3	cervix:	n/a	n/a
22	CTCF	chr6:33586980-33587130	AG04449	skin:	n/a	n/a
23	CTCF	chr6:33586920-33587070	HRE	kidney:	n/a	n/a
24	CTCF	chr6:33587058-33587181	MCF-7	breast:	n/a	n/a
25	CTCF	chr6:33587060-33587210	GM12867	blood:	n/a	n/a
26	CTCF	chr6:33587040-33587190	GM12874	blood:	n/a	n/a
27	CTCF	chr6:33587020-33587170	GM12875	blood:	n/a	n/a
28	CTCF	chr6:33587020-33587170	GM12870	blood:	n/a	n/a
29	CTCF	chr6:33587049-33587190	MCF-7	breast:	n/a	n/a
30	CTCF	chr6:33587040-33587190	GM12871	blood:	n/a	n/a
31	CTCF	chr6:33587040-33587190	HEEpiC	esophagus:	n/a	n/a
32	CTCF	chr6:33587040-33587190	HMEC	breast:	n/a	n/a
33	CTCF	chr6:33587000-33587150	GM12869	blood:	n/a	n/a
34	CTCF	chr6:33587035-33587207	MCF-7	breast:	n/a	n/a
35	CTCF	chr6:33587065-33587141	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr6:33587020-33587170	AG04449	skin:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:56735246..56737826-chr6:33586590..33589099,2	MCF-7	breast:
2	chr6:33550022..33555745-chr6:33586647..33590467,5	MCF-7	breast:

No data

Variant related genes	Relation type
ITPR3	TF binding region
ENSG00000204188	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12525769	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12526100	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs12529825	0.82[AMR][1000 genomes]
rs13197265	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13203795	0.94[EUR][1000 genomes]
rs13206871	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs188340	0.84[ASN][1000 genomes]
rs210211	0.84[ASN][1000 genomes]
rs34213779	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs422652	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs494835	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs71565395	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs71565398	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71565399	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462896	chr6:33534880-33588147	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv602833	chr6:33534880-33588147	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885770	chr6:33543409-33614127	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
5	nsv5250	chr6:33565017-33598370	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
6	esv3471778	chr6:33581874-33587572	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv3502822	chr6:33582379-33587443	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	esv1814733	chr6:33584788-33587443	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	esv1822053	chr6:33584788-33587443	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	esv1822157	chr6:33584788-33587443	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	esv1817557	chr6:33584788-33614127	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33578800-33588000	Weak transcription	Gastric	stomach
2	chr6:33579400-33588000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:33580000-33587600	Weak transcription	Brain Substantia Nigra	brain
4	chr6:33581600-33588000	Weak transcription	Brain Anterior Caudate	brain
5	chr6:33582000-33587400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:33582000-33587400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:33582000-33587400	Weak transcription	NHLF	lung
8	chr6:33582200-33587200	Enhancers	Hela-S3	cervix
9	chr6:33582200-33587800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:33582400-33587200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:33582400-33587200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:33583800-33587800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:33584000-33587800	Enhancers	Fetal Intestine Small	intestine
14	chr6:33585000-33587200	Weak transcription	K562	blood
15	chr6:33585200-33587600	Weak transcription	Osteobl	bone
16	chr6:33585400-33587200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr6:33585400-33587400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:33586000-33587200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:33586000-33587400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:33586000-33587600	Enhancers	HSMM	muscle
21	chr6:33586000-33588000	Enhancers	Spleen	Spleen
22	chr6:33586400-33587800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr6:33586600-33587200	Enhancers	HUVEC	blood vessel
24	chr6:33586600-33587200	Enhancers	NHDF-Ad	bronchial
25	chr6:33586600-33587400	Enhancers	Dnd41	blood
26	chr6:33586600-33587600	Enhancers	Fetal Lung	lung
27	chr6:33586600-33587600	Enhancers	HMEC	breast
28	chr6:33586600-33587800	Enhancers	Primary T cells from cord blood	blood
29	chr6:33586600-33587800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:33586600-33587800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr6:33586600-33587800	Enhancers	Fetal Intestine Large	intestine
32	chr6:33586600-33587800	Enhancers	Placenta	Placenta
33	chr6:33586600-33587800	Enhancers	Fetal Thymus	thymus
34	chr6:33586600-33587800	Enhancers	Right Ventricle	heart
35	chr6:33586600-33587800	Enhancers	NHEK	skin
36	chr6:33586600-33588200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:33586800-33587200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:33586800-33587400	Enhancers	A549	lung
39	chr6:33586800-33587600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
40	chr6:33586800-33587600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
41	chr6:33586800-33587600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
42	chr6:33586800-33587600	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr6:33586800-33587600	Enhancers	Duodenum Mucosa	Duodenum
44	chr6:33586800-33587800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:33586800-33587800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr6:33586800-33587800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr6:33586800-33587800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr6:33586800-33587800	Enhancers	Colonic Mucosa	Colon
49	chr6:33586800-33587800	Enhancers	Fetal Muscle Trunk	muscle
50	chr6:33586800-33587800	Enhancers	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links