Variant report

Variant	rs1954714
Chromosome Location	chr8:110622831-110622832
allele	A/G
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	GATA2	chr8:110622713-110623898	SH-SY5Y	brain:	n/a	chr8:110623727-110623744
3	KAP1	chr8:110622784-110624262	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:110619630..110621683-chr8:110622030..110624144,3	MCF-7	breast:
2	chr8:110612107..110614990-chr8:110621772..110623731,2	MCF-7	breast:
3	chr8:110616434..110618096-chr8:110622411..110624046,2	MCF-7	breast:
4	chr8:110615659..110617525-chr8:110621705..110624806,3	K562	blood:
5	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: 7 )

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

rs_ID	r²[population]
rs10095412	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13253969	0.84[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];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13254967	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16879844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[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]
rs2022930	1.00[CHB][hapmap];0.90[CHD][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];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703381	0.97[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[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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844239	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]
rs2844240	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]
rs2844241	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];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844242	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[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	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];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844245	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]
rs2844246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[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];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844248	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844249	0.94[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];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.93[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];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[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];0.88[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];0.88[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];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469274	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6982034	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[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];0.84[YRI][hapmap];0.93[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];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7003744	0.86[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];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7825702	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656885	0.88[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1954714	KCNV1	cis	lymphoblastoid	seeQTL
rs1954714	PKHD1L1	cis	multi-tissue	Pritchard
rs1954714	SYBU	cis	cerebellum	SCAN
rs1954714	PKHD1L1	cis	lymphoblastoid	seeQTL
rs1954714	EBAG9	cis	parietal	SCAN
rs1954714	PKHD1L1	cis	Lymphoblastoid	GTEx
rs1954714	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

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	chr8:110615600-110623000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr8:110616200-110623000	Weak transcription	Adipose Nuclei	Adipose
5	chr8:110617200-110625800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:110617200-110626600	Weak transcription	Right Atrium	heart
7	chr8:110617400-110632800	Weak transcription	Gastric	stomach
8	chr8:110617800-110632800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr8:110618400-110625400	Weak transcription	GM12878-XiMat	blood
10	chr8:110619800-110623000	Weak transcription	Colon Smooth Muscle	Colon
11	chr8:110619800-110623200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr8:110620000-110623200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr8:110620200-110623800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr8:110620400-110623000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr8:110620400-110623000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr8:110620400-110623000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr8:110620400-110623000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr8:110620400-110623200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr8:110620400-110623200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr8:110620400-110623200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr8:110620400-110623200	Weak transcription	Brain Hippocampus Middle	brain
22	chr8:110620400-110626000	Weak transcription	Brain Angular Gyrus	brain
23	chr8:110620400-110631000	Weak transcription	Pancreas	Pancrea
24	chr8:110620400-110632200	Weak transcription	HMEC	breast
25	chr8:110620400-110632800	Weak transcription	Brain Substantia Nigra	brain
26	chr8:110620400-110651200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr8:110620400-110654800	Weak transcription	Esophagus	oesophagus
28	chr8:110620800-110625800	Weak transcription	Brain Anterior Caudate	brain
29	chr8:110621000-110625800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr8:110621200-110623200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr8:110621200-110654800	Weak transcription	Fetal Brain Female	brain
32	chr8:110621600-110623600	Enhancers	HepG2	liver
33	chr8:110621600-110625800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr8:110622200-110623400	Strong transcription	Stomach Smooth Muscle	stomach
35	chr8:110622200-110624800	Enhancers	Fetal Intestine Large	intestine
36	chr8:110622200-110625000	Enhancers	Fetal Intestine Small	intestine
37	chr8:110622200-110632000	Strong transcription	Liver	Liver
38	chr8:110622400-110623200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr8:110622400-110623200	Strong transcription	NHEK	skin
40	chr8:110622400-110623400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr8:110622600-110623600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr8:110622600-110623600	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr8:110622600-110624000	Enhancers	Fetal Kidney	kidney
44	chr8:110622600-110624600	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr8:110622600-110635200	Weak transcription	Fetal Brain Male	brain
46	chr8:110622800-110623400	Enhancers	Small Intestine	intestine
47	chr8:110622800-110623600	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr8:110622800-110623600	Enhancers	Fetal Muscle Leg	muscle
49	chr8:110622800-110624200	Enhancers	K562	blood
50	chr8:110622800-110624400	Enhancers	Hela-S3	cervix

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