Variant report

Variant	rs2844245
Chromosome Location	chr8:110627005-110627006
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:110626045..110628361-chr8:110643151..110644803,2	MCF-7	breast:
2	chr8:110619143..110621265-chr8:110625482..110627368,2	MCF-7	breast:
3	chr8:110618290..110622116-chr8:110622585..110627832,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147642	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10095412	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13253969	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13254530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13254967	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16879844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1954713	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1954714	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2022930	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2154656	0.87[ASN][1000 genomes]
rs2703379	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703381	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703383	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2703391	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844241	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];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844242	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844243	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2844244	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844248	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844249	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844250	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs34147744	0.85[ASN][1000 genomes]
rs35642643	0.84[ASN][1000 genomes]
rs4367512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61152293	0.99[ASN][1000 genomes]
rs6469270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469274	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6982034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6994349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7003380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7003744	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7813979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7825702	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656885	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	esv1849702	chr8:110594148-110683804	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2844245	PKHD1L1	cis	lymphoblastoid	seeQTL
rs2844245	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL
rs2844245	SYBU	cis	cerebellum	SCAN
rs2844245	PKHD1L1	cis	multi-tissue	Pritchard
rs2844245	EBAG9	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110590200-110654800	Weak transcription	Lung	lung
2	chr8:110617400-110632800	Weak transcription	Gastric	stomach
3	chr8:110617800-110632800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr8:110620400-110631000	Weak transcription	Pancreas	Pancrea
5	chr8:110620400-110632200	Weak transcription	HMEC	breast
6	chr8:110620400-110632800	Weak transcription	Brain Substantia Nigra	brain
7	chr8:110620400-110651200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:110620400-110654800	Weak transcription	Esophagus	oesophagus
9	chr8:110621200-110654800	Weak transcription	Fetal Brain Female	brain
10	chr8:110622200-110632000	Strong transcription	Liver	Liver
11	chr8:110622600-110635200	Weak transcription	Fetal Brain Male	brain
12	chr8:110622800-110628000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr8:110623000-110637800	Weak transcription	Left Ventricle	heart
14	chr8:110623200-110628800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr8:110623200-110629400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr8:110623400-110635200	Weak transcription	Small Intestine	intestine
17	chr8:110623400-110655000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr8:110623600-110632800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr8:110624000-110628600	Weak transcription	Adipose Nuclei	Adipose
20	chr8:110624200-110634600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr8:110624600-110628800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr8:110624800-110628800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr8:110625000-110633000	Weak transcription	Ovary	ovary
24	chr8:110625600-110627200	Enhancers	Fetal Kidney	kidney
25	chr8:110626000-110627200	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr8:110626000-110627200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr8:110626000-110627400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr8:110626000-110627400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr8:110626000-110627400	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr8:110626200-110654800	Weak transcription	Brain Anterior Caudate	brain
31	chr8:110626400-110627200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr8:110626600-110627200	Enhancers	Right Atrium	heart
33	chr8:110626600-110627400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr8:110626600-110627600	Enhancers	Brain Angular Gyrus	brain
35	chr8:110626600-110632600	Weak transcription	Hela-S3	cervix
36	chr8:110626600-110633800	Weak transcription	HepG2	liver
37	chr8:110626800-110627400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr8:110626800-110630000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr8:110627000-110627200	Genic enhancers	NHEK	skin
40	chr8:110627000-110629400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr8:110627000-110630000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr8:110627000-110631400	Strong transcription	Stomach Smooth Muscle	stomach
43	chr8:110627000-110633800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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