Variant report

Variant	rs213235
Chromosome Location	chr6:28324757-28324758
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr6:28324616-28325306	IMR90	lung:	n/a	n/a
2	POLR2A	chr6:28321625-28325043	SK-N-MC	brain:	n/a	n/a
3	SETDB1	chr6:28324421-28325132	K562	blood:	n/a	n/a
4	POLR2A	chr6:28324670-28325346	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr6:28323469-28325125	HUVEC	blood vessel:	n/a	n/a
6	MAX	chr6:28324720-28325175	K562	blood:	n/a	n/a
7	POLR2A	chr6:28321678-28325465	K562	blood:	n/a	n/a
8	CBX3	chr6:28323339-28325251	K562	blood:	n/a	n/a
9	KAP1	chr6:28324450-28325419	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28303323..28305430-chr6:28323198..28325730,3	MCF-7	breast:
2	chr6:28247781..28251138-chr6:28322226..28325499,4	K562	blood:
3	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
4	chr6:27780093..27783062-chr6:28322537..28324933,2	K562	blood:
5	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
6	chr6:28102868..28106057-chr6:28324401..28327224,3	K562	blood:
7	chr6:27856204..27858764-chr6:28323949..28325832,2	K562	blood:
8	chr6:28219780..28221874-chr6:28323231..28325438,2	K562	blood:
9	chr6:27857264..27863272-chr6:28318615..28325449,9	K562	blood:
10	chr6:28109157..28111504-chr6:28323298..28325916,3	K562	blood:

No data

Variant related genes	Relation type
ZSCAN31	TF binding region
ENSG00000269293	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000182611	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000196374	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000196331	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1015810	0.91[EUR][1000 genomes]
rs1150669	0.91[EUR][1000 genomes]
rs1150671	0.91[EUR][1000 genomes]
rs11965542	1.00[EUR][1000 genomes]
rs11966042	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11966237	1.00[EUR][1000 genomes]
rs11967622	0.91[EUR][1000 genomes]
rs11969150	1.00[EUR][1000 genomes]
rs11970404	0.91[EUR][1000 genomes]
rs12333002	0.82[EUR][1000 genomes]
rs1233667	0.91[EUR][1000 genomes]
rs1233698	0.91[EUR][1000 genomes]
rs1233702	0.91[EUR][1000 genomes]
rs2078422	0.91[EUR][1000 genomes]
rs213227	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2159274	0.91[EUR][1000 genomes]
rs2232439	0.82[EUR][1000 genomes]
rs2531801	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531802	0.91[EUR][1000 genomes]
rs2531812	0.91[EUR][1000 genomes]
rs2531816	0.82[EUR][1000 genomes]
rs2531819	0.91[EUR][1000 genomes]
rs2531826	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531828	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382592	0.82[EUR][1000 genomes]
rs2859349	0.91[EUR][1000 genomes]
rs2859350	0.91[EUR][1000 genomes]
rs2859353	0.82[EUR][1000 genomes]
rs2859354	0.91[EUR][1000 genomes]
rs2859359	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859362	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2859367	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2859371	0.91[EUR][1000 genomes]
rs2859376	0.91[EUR][1000 genomes]
rs2859377	0.91[EUR][1000 genomes]
rs2859378	0.91[EUR][1000 genomes]
rs385908	0.91[EUR][1000 genomes]
rs400987	0.91[EUR][1000 genomes]
rs403774	0.91[EUR][1000 genomes]
rs423118	0.91[EUR][1000 genomes]
rs59457415	1.00[EUR][1000 genomes]
rs61540948	0.91[EUR][1000 genomes]
rs62638680	1.00[EUR][1000 genomes]
rs6908414	0.91[EUR][1000 genomes]
rs6910942	0.91[EUR][1000 genomes]
rs6916243	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928131	0.91[EUR][1000 genomes]
rs6932313	0.91[EUR][1000 genomes]
rs6932394	1.00[EUR][1000 genomes]
rs719370	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73385806	1.00[EUR][1000 genomes]
rs73385807	1.00[EUR][1000 genomes]
rs73385810	1.00[EUR][1000 genomes]
rs73385818	1.00[EUR][1000 genomes]
rs73385870	1.00[EUR][1000 genomes]
rs73387810	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73398516	0.91[EUR][1000 genomes]
rs73399084	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73400525	0.91[EUR][1000 genomes]
rs73400579	0.91[EUR][1000 genomes]
rs73400580	1.00[EUR][1000 genomes]
rs73400590	1.00[EUR][1000 genomes]
rs73401012	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73401666	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73402513	1.00[EUR][1000 genomes]
rs7739389	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7752608	0.91[ASN][1000 genomes]
rs7759845	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9468291	0.91[EUR][1000 genomes]
rs9468293	0.91[EUR][1000 genomes]
rs9468305	0.91[EUR][1000 genomes]
rs9468306	0.91[EUR][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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28318400-28332000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:28318400-28350800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:28323000-28324800	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr6:28323000-28325000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:28323200-28325000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr6:28323600-28324800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:28324000-28324800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:28324000-28324800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr6:28324000-28324800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:28324000-28324800	Enhancers	Lung	lung
11	chr6:28324000-28324800	Flanking Active TSS	Hela-S3	cervix
12	chr6:28324000-28325200	Enhancers	Gastric	stomach
13	chr6:28324000-28325600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:28324200-28324800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:28324200-28324800	Enhancers	Ovary	ovary
16	chr6:28324200-28324800	Flanking Active TSS	Rectal Smooth Muscle	rectum
17	chr6:28324200-28324800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr6:28324200-28325000	Enhancers	Primary B cells from peripheral blood	blood
19	chr6:28324200-28325200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr6:28324200-28325200	Enhancers	Right Ventricle	heart
21	chr6:28324200-28325600	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr6:28324200-28325600	Enhancers	HUVEC	blood vessel
23	chr6:28324200-28328600	Weak transcription	Primary B cells from cord blood	blood
24	chr6:28324200-28331600	Weak transcription	Thymus	Thymus
25	chr6:28324400-28324800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:28324400-28324800	Enhancers	Liver	Liver
27	chr6:28324400-28324800	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr6:28324400-28324800	Enhancers	Esophagus	oesophagus
29	chr6:28324400-28325000	Enhancers	HMEC	breast
30	chr6:28324400-28325200	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr6:28324400-28325200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr6:28324400-28325200	Enhancers	Muscle Satellite Cultured Cells	--
33	chr6:28324400-28325200	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr6:28324400-28325200	Enhancers	Stomach Mucosa	stomach
35	chr6:28324400-28325400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:28324400-28325400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr6:28324400-28325400	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr6:28324400-28325600	Enhancers	K562	blood
39	chr6:28324400-28325800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:28324400-28326400	Weak transcription	Fetal Muscle Leg	muscle
41	chr6:28324400-28326800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:28324400-28326800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:28324400-28326800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:28324400-28327000	Weak transcription	Placenta	Placenta
45	chr6:28324400-28327400	Weak transcription	Primary T cells from cord blood	blood
46	chr6:28324400-28327400	Weak transcription	Fetal Intestine Large	intestine
47	chr6:28324400-28327800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr6:28324400-28328200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:28324400-28328800	Weak transcription	Brain Anterior Caudate	brain
50	chr6:28324400-28329600	Weak transcription	Aorta	Aorta

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