Variant report

Variant	rs2844239
Chromosome Location	chr8:110624179-110624180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr8:110622433-110624888	HEK293	kidney:	n/a	n/a
2	TCF7L2	chr8:110623368-110624500	PANC-1	pancreas:	n/a	chr8:110624263-110624270
3	EP300	chr8:110622848-110624213	SK-N-SH	brain:	n/a	chr8:110623593-110623601
4	TCF7L2	chr8:110623147-110624751	HEK293	kidney:	n/a	chr8:110624263-110624270
5	KAP1	chr8:110622784-110624262	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:110615659..110617525-chr8:110621705..110624806,3	K562	blood:
2	chr8:110623120..110625738-chr8:110638135..110640971,2	K562	blood:
3	chr8:110618290..110622116-chr8:110622585..110627832,7	MCF-7	breast:

Variant related genes	Relation type
SYBU	TF binding region
ENSG00000147642	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10095412	0.90[AMR][1000 genomes];0.92[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	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16879844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1954713	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1954714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2022930	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2154656	0.87[ASN][1000 genomes]
rs2703379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703381	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703383	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2703391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844242	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844245	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]
rs2844246	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]
rs2844247	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]
rs2844248	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844249	0.96[AMR][1000 genomes];0.99[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[JPT][hapmap];0.92[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[JPT][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];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6982034	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]
rs6994349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[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];0.91[AMR][1000 genomes];0.97[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];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7825702	0.90[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2844239	PKHD1L1	cis	Lymphoblastoid	GTEx
rs2844239	PKHD1L1	cis	multi-tissue	Pritchard
rs2844239	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110590200-110654800	Weak transcription	Lung	lung
2	chr8:110612200-110624200	Weak transcription	Aorta	Aorta
3	chr8:110617200-110625800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:110617200-110626600	Weak transcription	Right Atrium	heart
5	chr8:110617400-110632800	Weak transcription	Gastric	stomach
6	chr8:110617800-110632800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr8:110618400-110625400	Weak transcription	GM12878-XiMat	blood
8	chr8:110620400-110626000	Weak transcription	Brain Angular Gyrus	brain
9	chr8:110620400-110631000	Weak transcription	Pancreas	Pancrea
10	chr8:110620400-110632200	Weak transcription	HMEC	breast
11	chr8:110620400-110632800	Weak transcription	Brain Substantia Nigra	brain
12	chr8:110620400-110651200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr8:110620400-110654800	Weak transcription	Esophagus	oesophagus
14	chr8:110620800-110625800	Weak transcription	Brain Anterior Caudate	brain
15	chr8:110621000-110625800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr8:110621200-110654800	Weak transcription	Fetal Brain Female	brain
17	chr8:110621600-110625800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr8:110622200-110624800	Enhancers	Fetal Intestine Large	intestine
19	chr8:110622200-110625000	Enhancers	Fetal Intestine Small	intestine
20	chr8:110622200-110632000	Strong transcription	Liver	Liver
21	chr8:110622600-110624600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr8:110622600-110635200	Weak transcription	Fetal Brain Male	brain
23	chr8:110622800-110624200	Enhancers	K562	blood
24	chr8:110622800-110624400	Enhancers	Hela-S3	cervix
25	chr8:110622800-110624800	Enhancers	Duodenum Mucosa	Duodenum
26	chr8:110622800-110628000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr8:110623000-110624200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr8:110623000-110624200	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr8:110623000-110625000	Enhancers	Ovary	ovary
30	chr8:110623000-110637800	Weak transcription	Left Ventricle	heart
31	chr8:110623200-110624600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr8:110623200-110625800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr8:110623200-110628800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr8:110623200-110629400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr8:110623400-110625400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr8:110623400-110627000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr8:110623400-110635200	Weak transcription	Small Intestine	intestine
38	chr8:110623400-110655000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr8:110623600-110626000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr8:110623600-110626000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr8:110623600-110626000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr8:110623600-110626000	Weak transcription	HepG2	liver
43	chr8:110623600-110626200	Weak transcription	Colon Smooth Muscle	Colon
44	chr8:110623600-110626400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr8:110623600-110632800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr8:110623800-110626000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr8:110623800-110627000	Weak transcription	NHEK	skin
48	chr8:110624000-110624200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr8:110624000-110625600	Weak transcription	Fetal Kidney	kidney
50	chr8:110624000-110628600	Weak transcription	Adipose Nuclei	Adipose

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