Variant report

Variant	rs12180820
Chromosome Location	chr6:28316478-28316479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28249255..28252885-chr6:28315781..28319284,4	K562	blood:
2	chr6:28109689..28111250-chr6:28315546..28317991,2	K562	blood:
3	chr6:28301955..28305314-chr6:28311630..28316587,6	MCF-7	breast:
4	chr6:28166974..28169940-chr6:28315541..28317306,2	K562	blood:
5	chr6:28103114..28106211-chr6:28315199..28319125,3	K562	blood:
6	chr6:28314766..28319001-chr6:28320941..28324187,4	MCF-7	breast:
7	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
8	chr6:28127970..28130555-chr6:28316475..28318965,2	K562	blood:
9	chr6:27859494..27863644-chr6:28315287..28317995,4	K562	blood:
10	chr6:27859494..27861769-chr6:28315287..28317995,2	K562	blood:
11	chr6:28300850..28305636-chr6:28315212..28320749,12	MCF-7	breast:
12	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
13	chr6:28218194..28221046-chr6:28316270..28319035,4	K562	blood:
14	chr6:28299865..28301376-chr6:28315526..28317433,2	MCF-7	breast:
15	chr6:28219546..28223731-chr6:28316147..28319107,5	K562	blood:
16	chr6:28101857..28106060-chr6:28315199..28321034,6	K562	blood:
17	chr6:28315597..28319153-chr6:28366055..28369015,3	K562	blood:
18	chr6:28233021..28237962-chr6:28316234..28324041,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198315	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000226314	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000176933	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1016070	0.86[CHB][hapmap]
rs12000	0.86[CHB][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap]
rs1361386	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1416920	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893947	0.85[CHD][hapmap]
rs16893970	0.85[CHD][hapmap]
rs1997660	0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs2021745	0.86[CHB][hapmap]
rs2108926	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213230	0.81[CEU][hapmap]
rs2531813	0.86[CHB][hapmap]
rs2531814	0.86[CHB][hapmap]
rs2859372	0.86[CHB][hapmap]
rs2859373	0.86[CHB][hapmap]
rs2859374	0.86[CHB][hapmap]
rs4713158	0.85[EUR][1000 genomes]
rs6456815	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936644	0.92[ASN][1000 genomes]
rs6942030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707907	0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs758398	0.86[CHB][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7772827	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs853683	0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs853690	0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs853693	0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs9468333	0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs9468334	0.89[ASN][1000 genomes]
rs9468344	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs12180820	RP5-874C20.3	cis	Thyroid	GTEx
rs12180820	HLA-A	cis	multi-tissue	Pritchard
rs12180820	HIST1H2BO	cis	parietal	SCAN
rs12180820	ZKSCAN3	cis	cerebellum	SCAN
rs12180820	ZSCAN23	cis	Artery Tibial	GTEx
rs12180820	AL022393.7	cis	Esophagus Muscularis	GTEx
rs12180820	HIST1H2BN	cis	cerebellum	SCAN
rs12180820	ZSCAN23	cis	cerebellum	SCAN
rs12180820	AL022393.7	cis	Heart Left Ventricle	GTEx
rs12180820	ZSCAN23	cis	parietal	SCAN
rs12180820	ZSCAN31	cis	lung	GTEx
rs12180820	AL022393.7	cis	Muscle Skeletal	GTEx
rs12180820	ZNF192	cis	cerebellum	SCAN
rs12180820	HLA-H	cis	multi-tissue	Pritchard
rs12180820	ZNF187	cis	cerebellum	SCAN
rs12180820	ZNF323	cis	parietal	SCAN
rs12180820	NKAPL	cis	parietal	SCAN
rs12180820	ZKSCAN3	cis	parietal	SCAN
rs12180820	AL022393.7	cis	Nerve Tibial	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28304400-28317400	Weak transcription	Pancreas	Pancrea
2	chr6:28304800-28317200	Weak transcription	Aorta	Aorta
3	chr6:28305000-28317200	Weak transcription	Brain Anterior Caudate	brain
4	chr6:28305000-28317200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:28305200-28317000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:28305200-28317000	Weak transcription	NHEK	skin
7	chr6:28305200-28317200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:28305200-28317200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:28305200-28317200	Weak transcription	HSMMtube	muscle
10	chr6:28305800-28317200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:28315200-28317000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:28315200-28317200	Weak transcription	Psoas Muscle	Psoas
13	chr6:28315400-28317000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:28315400-28317200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:28315600-28317000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:28315600-28317200	Weak transcription	K562	blood

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