Variant report

Variant	rs6921919
Chromosome Location	chr6:28325201-28325202
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 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	chr6:28324670-28325346	HUVEC	blood vessel:	n/a	n/a
3	MAFK	chr6:28324810-28325216	IMR90	lung:	n/a	chr6:28324953-28324968
4	POLR2A	chr6:28321678-28325465	K562	blood:	n/a	n/a
5	POLR2A	chr6:28324815-28325317	HepG2	liver:	n/a	n/a
6	CBX3	chr6:28323339-28325251	K562	blood:	n/a	n/a
7	KAP1	chr6:28324450-28325419	K562	blood:	n/a	n/a

No data

(count:9 , 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	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
5	chr6:28102868..28106057-chr6:28324401..28327224,3	K562	blood:
6	chr6:27856204..27858764-chr6:28323949..28325832,2	K562	blood:
7	chr6:28219780..28221874-chr6:28323231..28325438,2	K562	blood:
8	chr6:27857264..27863272-chr6:28318615..28325449,9	K562	blood:
9	chr6:28109157..28111504-chr6:28323298..28325916,3	K562	blood:

No data

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

Extended variants
information (count: 36 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1119211	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11756111	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs11758148	1.00[JPT][hapmap]
rs11758337	1.00[JPT][hapmap]
rs11970439	0.88[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs13210258	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs1474589	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.82[MKK][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16893937	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs16894116	0.89[CEU][hapmap];0.84[YRI][hapmap];0.86[EUR][1000 genomes]
rs16901847	0.89[CEU][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17301128	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs17312661	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs17776284	1.00[JPT][hapmap]
rs213230	0.82[ASW][hapmap];0.81[MEX][hapmap]
rs2185955	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2232428	0.81[ASW][hapmap];0.90[LWK][hapmap];0.82[MKK][hapmap];0.84[YRI][hapmap]
rs2235358	1.00[JPT][hapmap]
rs2235359	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2299031	1.00[JPT][hapmap]
rs35875412	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3800326	1.00[JPT][hapmap]
rs56131013	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6456814	0.82[EUR][1000 genomes]
rs6456816	0.81[EUR][1000 genomes]
rs6903652	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6903823	0.94[CEU][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6912584	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs6922111	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71559082	0.86[EUR][1000 genomes]
rs73742542	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7765989	0.86[EUR][1000 genomes]
rs7766356	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs7769054	1.00[JPT][hapmap]
rs9468350	0.86[EUR][1000 genomes]
rs993619	1.00[JPT][hapmap]

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

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs6921919	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs6921919	ZSCAN23	cis	cerebellum	SCAN
rs6921919	ZNF192	cis	cerebellum	SCAN
rs6921919	ZSCAN23	cis	parietal	SCAN
rs6921919	ZNF187	cis	cerebellum	SCAN
rs6921919	ZKSCAN3	cis	parietal	SCAN
rs6921919	AL022393.7	cis	Muscle Skeletal	GTEx
rs6921919	HLA-A	cis	multi-tissue	Pritchard
rs6921919	ZKSCAN3	cis	cerebellum	SCAN
rs6921919	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs6921919	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs6921919	ZSCAN23	cis	Artery Tibial	GTEx
rs6921919	HLA-H	cis	multi-tissue	Pritchard
rs6921919	ZNF323	cis	parietal	SCAN

Chromatin state (count:125 , 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	chr6:28324000-28325600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:28324200-28325600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr6:28324200-28325600	Enhancers	HUVEC	blood vessel
6	chr6:28324200-28328600	Weak transcription	Primary B cells from cord blood	blood
7	chr6:28324200-28331600	Weak transcription	Thymus	Thymus
8	chr6:28324400-28325400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:28324400-28325400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:28324400-28325400	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr6:28324400-28325600	Enhancers	K562	blood
12	chr6:28324400-28325800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:28324400-28326400	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:28324400-28326800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:28324400-28326800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:28324400-28326800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:28324400-28327000	Weak transcription	Placenta	Placenta
18	chr6:28324400-28327400	Weak transcription	Primary T cells from cord blood	blood
19	chr6:28324400-28327400	Weak transcription	Fetal Intestine Large	intestine
20	chr6:28324400-28327800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr6:28324400-28328200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:28324400-28328800	Weak transcription	Brain Anterior Caudate	brain
23	chr6:28324400-28329600	Weak transcription	Aorta	Aorta
24	chr6:28324400-28329600	Weak transcription	Fetal Intestine Small	intestine
25	chr6:28324400-28330600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:28324400-28330800	Weak transcription	Brain Substantia Nigra	brain
27	chr6:28324400-28331000	Weak transcription	Psoas Muscle	Psoas
28	chr6:28324400-28331000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:28324400-28331200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:28324400-28331600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:28324400-28332600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:28324400-28333000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr6:28324400-28333000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr6:28324400-28333200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:28324400-28336000	Weak transcription	GM12878-XiMat	blood
36	chr6:28324400-28347600	Weak transcription	NHDF-Ad	bronchial
37	chr6:28324400-28347800	Weak transcription	Fetal Brain Male	brain
38	chr6:28324400-28348200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr6:28324400-28357200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:28324400-28357600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr6:28324600-28326800	Weak transcription	Adipose Nuclei	Adipose
42	chr6:28324600-28327000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr6:28324600-28327000	Weak transcription	Fetal Stomach	stomach
44	chr6:28324600-28327200	Weak transcription	Brain Germinal Matrix	brain
45	chr6:28324600-28327200	Weak transcription	Fetal Brain Female	brain
46	chr6:28324600-28327200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr6:28324600-28327200	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr6:28324600-28328200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr6:28324600-28328200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:28324600-28328200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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