Variant report

Variant	rs2980571
Chromosome Location	chr8:110348249-110348250
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr8:110348223-110348351	K562	blood:	n/a	n/a
2	FAM48A	chr8:110348146-110348593	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:110346229..110349558-chr8:110551131..110555531,7	K562	blood:
2	chr8:110344786..110348564-chr8:110349076..110353866,8	MCF-7	breast:
3	chr8:109930677..109932392-chr8:110345259..110348256,2	MCF-7	breast:
4	chr8:110296774..110299286-chr8:110348162..110350315,2	K562	blood:
5	chr8:110344899..110348479-chr8:110652629..110655762,4	MCF-7	breast:

No data

Variant related genes	Relation type
NUDCD1	TF binding region
ENY2	TF binding region
ENSG00000147654	Chromatin interaction
ENSG00000147642	Chromatin interaction
ENSG00000253796	Chromatin interaction
ENSG00000120533	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11998321	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13439864	0.82[CEU][hapmap]
rs1673383	0.86[MEX][hapmap]
rs1673384	0.86[MEX][hapmap]
rs1673409	0.90[MEX][hapmap]
rs1673412	0.91[MEX][hapmap]
rs1673413	0.86[MEX][hapmap]
rs1783169	0.91[MEX][hapmap]
rs1870389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2022935	0.91[MEX][hapmap]
rs2607624	0.86[MEX][hapmap]
rs2844261	0.86[MEX][hapmap]
rs2926229	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2926230	0.81[ASN][1000 genomes]
rs2926232	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2926233	0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2926234	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2926237	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2926239	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2926242	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2980585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980586	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891273	chr8:110219735-110475874	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv891279	chr8:110268104-110450092	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv891280	chr8:110346363-110465481	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2980571	PKHD1L1	cis	Lymphoblastoid	GTEx
rs2980571	PKHD1L1	cis	multi-tissue	Pritchard
rs2980571	PKHD1L1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110344400-110348400	Active TSS	Right Ventricle	heart
2	chr8:110347000-110358200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr8:110347000-110358400	Weak transcription	Spleen	Spleen
4	chr8:110347000-110358800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr8:110347200-110354800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:110347200-110355000	Weak transcription	Lung	lung
7	chr8:110347200-110357600	Weak transcription	Pancreas	Pancrea
8	chr8:110347200-110358200	Weak transcription	Esophagus	oesophagus
9	chr8:110347200-110359800	Weak transcription	Gastric	stomach
10	chr8:110347400-110348400	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr8:110347400-110348400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr8:110347400-110348600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr8:110347400-110349200	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr8:110347400-110349200	Weak transcription	Left Ventricle	heart
15	chr8:110347400-110349400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr8:110347400-110349800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr8:110347400-110350000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr8:110347400-110351200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr8:110347400-110356200	Weak transcription	Ovary	ovary
20	chr8:110347400-110358000	Weak transcription	Colonic Mucosa	Colon
21	chr8:110347400-110358400	Weak transcription	Fetal Brain Male	brain
22	chr8:110347400-110359400	Weak transcription	Aorta	Aorta
23	chr8:110347400-110359400	Weak transcription	Brain Substantia Nigra	brain
24	chr8:110347400-110360000	Weak transcription	Stomach Mucosa	stomach
25	chr8:110347600-110348400	Enhancers	Primary T cells from cord blood	blood
26	chr8:110347600-110348400	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr8:110347600-110348400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr8:110347600-110348400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr8:110347600-110348400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr8:110347600-110348400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr8:110347600-110348400	Enhancers	Fetal Muscle Leg	muscle
32	chr8:110347600-110348400	Weak transcription	HSMM	muscle
33	chr8:110347600-110348600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr8:110347600-110348600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr8:110347600-110348600	Enhancers	Liver	Liver
36	chr8:110347600-110348600	Enhancers	Duodenum Mucosa	Duodenum
37	chr8:110347600-110348600	Enhancers	Osteobl	bone
38	chr8:110347600-110348800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr8:110347600-110348800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr8:110347600-110348800	Enhancers	Hela-S3	cervix
41	chr8:110347600-110348800	Weak transcription	NHLF	lung
42	chr8:110347600-110349000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr8:110347600-110349000	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr8:110347600-110349400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr8:110347600-110349800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr8:110347600-110350000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr8:110347600-110350200	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr8:110347600-110350400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr8:110347600-110354800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr8:110347600-110354800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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