Variant report

Variant	rs2980583
Chromosome Location	chr8:110358691-110358692
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:110356952..110358938-chr8:110359155..110360701,2	K562	blood:
2	chr8:110358079..110360287-chr8:110586276..110588279,2	K562	blood:
3	chr8:110357743..110359361-chr8:110551222..110553021,2	MCF-7	breast:
4	chr8:110357510..110359892-chr8:110365729..110367920,2	K562	blood:
5	chr8:110353436..110355204-chr8:110357328..110360216,4	K562	blood:
6	chr8:110356416..110359294-chr8:110548274..110550933,2	MCF-7	breast:
7	chr8:110357096..110359808-chr8:110548586..110553351,4	K562	blood:
8	chr8:110358379..110359744-chr8:110664444..110665358,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000147654	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10098672	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10099126	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1037695	0.89[EUR][1000 genomes]
rs12334438	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13278812	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1379369	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1379370	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1457287	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1457289	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1457290	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1457291	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1458918	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1458919	0.99[ASN][1000 genomes]
rs1585294	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1870107	0.84[EUR][1000 genomes]
rs1870109	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2061294	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2061295	0.89[EUR][1000 genomes]
rs2199120	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2926224	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2926225	0.94[ASN][1000 genomes]
rs2926228	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2926236	0.83[EUR][1000 genomes]
rs2926238	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980569	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980575	0.99[ASN][1000 genomes]
rs2980582	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4604408	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4735133	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6469256	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6469257	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6469260	0.88[EUR][1000 genomes]
rs6651203	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6982748	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6987198	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6993467	0.82[EUR][1000 genomes]
rs7002606	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7002926	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7818553	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7819151	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs897838	0.88[EUR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2980583	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL
rs2980583	PKHD1L1	cis	multi-tissue	Pritchard
rs2980583	PKHD1L1	cis	Nerve Tibial	GTEx
rs2980583	RP11-419L20.2	cis	Thyroid	GTEx
rs2980583	PKHD1L1	cis	Thyroid	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110347000-110358800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:110347200-110359800	Weak transcription	Gastric	stomach
3	chr8:110347400-110359400	Weak transcription	Aorta	Aorta
4	chr8:110347400-110359400	Weak transcription	Brain Substantia Nigra	brain
5	chr8:110347400-110360000	Weak transcription	Stomach Mucosa	stomach
6	chr8:110348400-110360200	Weak transcription	Fetal Intestine Small	intestine
7	chr8:110348800-110359600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr8:110348800-110364400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr8:110349600-110359400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr8:110353000-110361600	Weak transcription	NHDF-Ad	bronchial
11	chr8:110356000-110359400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr8:110356200-110359400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr8:110356400-110359400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr8:110356600-110358800	Weak transcription	A549	lung
15	chr8:110356600-110359000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr8:110356600-110359200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr8:110356600-110359400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr8:110356600-110359600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr8:110356800-110358800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr8:110356800-110358800	Weak transcription	HUVEC	blood vessel
21	chr8:110356800-110359200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr8:110356800-110359400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr8:110356800-110359400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr8:110356800-110359800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr8:110356800-110360200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr8:110357000-110358800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr8:110357000-110358800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr8:110357000-110358800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr8:110357000-110358800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr8:110357000-110358800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr8:110357000-110358800	Weak transcription	Brain Angular Gyrus	brain
32	chr8:110357000-110359000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr8:110357000-110359000	Weak transcription	Adipose Nuclei	Adipose
34	chr8:110357000-110359400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr8:110357000-110359400	Weak transcription	Brain Anterior Caudate	brain
36	chr8:110357000-110359600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr8:110357000-110360200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr8:110357200-110359000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr8:110357200-110359000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr8:110357200-110359000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr8:110357200-110359000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr8:110357200-110359200	Weak transcription	HepG2	liver
43	chr8:110357200-110359400	Weak transcription	Right Ventricle	heart
44	chr8:110357200-110359800	Weak transcription	HMEC	breast
45	chr8:110357200-110360000	Weak transcription	Primary T cells from cord blood	blood
46	chr8:110357200-110360000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr8:110357200-110360200	Weak transcription	Fetal Heart	heart
48	chr8:110357200-110360600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr8:110357200-110360600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr8:110357200-110360600	Weak transcription	K562	blood

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