Variant report

Variant	rs2980582
Chromosome Location	chr8:110358242-110358243
allele	C/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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:110356952..110358938-chr8:110359155..110360701,2	K562	blood:
2	chr8:110356353..110358345-chr8:110361451..110363405,2	MCF-7	breast:
3	chr8:110356541..110358567-chr8:110652716..110654323,2	K562	blood:
4	chr8:110355589..110358596-chr8:110550542..110552527,3	K562	blood:
5	chr8:110358079..110360287-chr8:110586276..110588279,2	K562	blood:
6	chr8:110357743..110359361-chr8:110551222..110553021,2	MCF-7	breast:
7	chr8:110357510..110359892-chr8:110365729..110367920,2	K562	blood:
8	chr8:110345424..110348480-chr8:110354425..110358647,4	MCF-7	breast:
9	chr8:110353436..110355204-chr8:110357328..110360216,4	K562	blood:
10	chr8:110356416..110359294-chr8:110548274..110550933,2	MCF-7	breast:
11	chr8:110356323..110358473-chr8:110658586..110660962,2	K562	blood:
12	chr8:110357096..110359808-chr8:110548586..110553351,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000120533	Chromatin interaction
ENSG00000120526	Chromatin interaction
ENSG00000147654	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10098672	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs10099126	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs1037695	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs12334438	0.90[CEU][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13278812	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs1379369	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs1379370	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs1457286	0.85[CEU][hapmap]
rs1457287	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs1457289	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs1457290	0.84[EUR][1000 genomes]
rs1457291	0.84[EUR][1000 genomes]
rs1458918	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1458919	0.96[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1585294	0.89[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1673407	0.81[CEU][hapmap]
rs1673408	0.81[CEU][hapmap]
rs1783144	0.81[CEU][hapmap]
rs1840908	0.82[CEU][hapmap]
rs1870107	0.84[CEU][hapmap]
rs1870109	0.84[EUR][1000 genomes]
rs2061294	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2061295	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2168679	0.82[CEU][hapmap]
rs2199120	0.92[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2349760	0.82[CEU][hapmap]
rs2926224	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2926225	0.91[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs2926228	0.93[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2926236	0.85[CEU][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes]
rs2926238	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980569	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980575	0.99[ASN][1000 genomes]
rs2980583	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4604408	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs4735133	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs6469256	0.84[EUR][1000 genomes]
rs6469257	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs6469260	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs6469261	0.93[YRI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6469262	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs6651203	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6982748	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs6987198	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6993467	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7002606	0.83[EUR][1000 genomes]
rs7002926	0.87[EUR][1000 genomes]
rs7818553	0.86[EUR][1000 genomes]
rs7819151	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs7840592	0.82[CEU][hapmap]
rs897838	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs921960	0.85[CEU][hapmap]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2980582	PKHD1L1	cis	Nerve Tibial	GTEx
rs2980582	PKHD1L1	cis	Thyroid	GTEx
rs2980582	PKHD1L1	cis	Lymphoblastoid	GTEx
rs2980582	RP11-419L20.2	cis	Thyroid	GTEx
rs2980582	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL
rs2980582	PKHD1L1	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110347000-110358400	Weak transcription	Spleen	Spleen
2	chr8:110347000-110358800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr8:110347200-110359800	Weak transcription	Gastric	stomach
4	chr8:110347400-110358400	Weak transcription	Fetal Brain Male	brain
5	chr8:110347400-110359400	Weak transcription	Aorta	Aorta
6	chr8:110347400-110359400	Weak transcription	Brain Substantia Nigra	brain
7	chr8:110347400-110360000	Weak transcription	Stomach Mucosa	stomach
8	chr8:110347600-110358400	Weak transcription	Fetal Stomach	stomach
9	chr8:110348000-110358400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr8:110348400-110360200	Weak transcription	Fetal Intestine Small	intestine
11	chr8:110348800-110358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr8:110348800-110359600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr8:110348800-110364400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr8:110349600-110359400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr8:110351200-110358400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr8:110351400-110358400	Weak transcription	Psoas Muscle	Psoas
17	chr8:110351600-110358400	Weak transcription	Small Intestine	intestine
18	chr8:110353000-110361600	Weak transcription	NHDF-Ad	bronchial
19	chr8:110353400-110358600	Weak transcription	NHLF	lung
20	chr8:110355600-110358600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr8:110355800-110358400	Weak transcription	Osteobl	bone
22	chr8:110356000-110359400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr8:110356200-110359400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr8:110356400-110359400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr8:110356600-110358400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr8:110356600-110358600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr8:110356600-110358600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr8:110356600-110358800	Weak transcription	A549	lung
29	chr8:110356600-110359000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr8:110356600-110359200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr8:110356600-110359400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr8:110356600-110359600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr8:110356800-110358400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr8:110356800-110358400	Weak transcription	NH-A	brain
35	chr8:110356800-110358600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr8:110356800-110358600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr8:110356800-110358600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr8:110356800-110358600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr8:110356800-110358600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr8:110356800-110358600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr8:110356800-110358600	Weak transcription	Colon Smooth Muscle	Colon
42	chr8:110356800-110358600	Weak transcription	Placenta	Placenta
43	chr8:110356800-110358600	Weak transcription	Ovary	ovary
44	chr8:110356800-110358600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr8:110356800-110358600	Weak transcription	Thymus	Thymus
46	chr8:110356800-110358600	Weak transcription	Dnd41	blood
47	chr8:110356800-110358800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr8:110356800-110358800	Weak transcription	HUVEC	blood vessel
49	chr8:110356800-110359200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr8:110356800-110359400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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