Variant report

Variant	rs13101580
Chromosome Location	chr4:175219813-175219814
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:175203637..175205285-chr4:175218500..175220643,2	K562	blood:

Variant related genes	Relation type
ENSG00000164118	Chromatin interaction
ENSG00000164117	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10034021	1.00[CHB][hapmap]
rs10565	1.00[CHB][hapmap]
rs11555602	1.00[JPT][hapmap]
rs11929798	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933187	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940726	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11940758	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11942947	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11944262	0.81[MEX][hapmap]
rs11947136	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs14278	1.00[JPT][hapmap]
rs17060409	1.00[JPT][hapmap]
rs17060445	1.00[JPT][hapmap]
rs17357120	0.89[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap]
rs1876515	0.87[CEU][hapmap]
rs2332836	0.92[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs34407356	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34888351	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35332594	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4287982	1.00[CHB][hapmap]
rs4695915	0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs4695918	0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs4695919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4695920	0.81[AMR][1000 genomes]
rs4695921	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4695922	1.00[CHB][hapmap]
rs6553777	0.80[YRI][hapmap]
rs68084371	0.85[AFR][1000 genomes]
rs6824643	0.94[MEX][hapmap]
rs6851312	0.94[MEX][hapmap]
rs7678305	0.83[MEX][hapmap];0.86[AMR][1000 genomes]
rs7681841	1.00[JPT][hapmap]
rs7692518	1.00[JPT][hapmap]
rs7697587	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016910	chr4:174952788-175349057	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537363	chr4:174952788-175349057	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv881449	chr4:174984230-175225452	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv596234	chr4:175053051-175361437	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13101580	KIAA1712	cis	parietal	SCAN
rs13101580	KIAA1712	Cis_1M	lymphoblastoid	RTeQTL
rs13101580	CEP44	cis	Esophagus Muscularis	GTEx
rs13101580	KIAA1712	cis	cerebellum	SCAN
rs13101580	CEP44	cis	Thyroid	GTEx
rs13101580	KIAA1712	cis	multi-tissue	Pritchard

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175205600-175241600	Weak transcription	Small Intestine	intestine
2	chr4:175206000-175235000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:175206200-175241000	Weak transcription	Right Ventricle	heart
4	chr4:175206400-175221800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:175206400-175228200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:175206600-175237800	Weak transcription	Osteobl	bone
7	chr4:175206800-175229200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr4:175206800-175241800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:175207000-175239000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:175207000-175240000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:175207000-175242000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:175207600-175220800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr4:175214200-175239200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr4:175214600-175220000	Weak transcription	Liver	Liver
15	chr4:175214600-175220200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr4:175214600-175220200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:175214600-175220200	Weak transcription	Fetal Thymus	thymus
18	chr4:175214600-175220200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr4:175214600-175220400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:175214600-175220400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:175214600-175220600	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr4:175214600-175220800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr4:175214600-175220800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr4:175214600-175220800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:175214600-175224400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr4:175214600-175224800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:175214600-175226400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr4:175214600-175228400	Weak transcription	Left Ventricle	heart
29	chr4:175214600-175229000	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:175214600-175230000	Weak transcription	Fetal Lung	lung
31	chr4:175214600-175230200	Weak transcription	Fetal Brain Male	brain
32	chr4:175214600-175233600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:175214600-175236000	Weak transcription	A549	lung
34	chr4:175214600-175237200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr4:175214600-175237400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:175214600-175238000	Weak transcription	HMEC	breast
37	chr4:175214600-175238400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr4:175214600-175238800	Weak transcription	Aorta	Aorta
39	chr4:175214600-175239000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr4:175214600-175239000	Weak transcription	HepG2	liver
41	chr4:175214600-175240000	Weak transcription	Colon Smooth Muscle	Colon
42	chr4:175214600-175240200	Weak transcription	Brain Angular Gyrus	brain
43	chr4:175214600-175240600	Weak transcription	Fetal Stomach	stomach
44	chr4:175214600-175241600	Weak transcription	Lung	lung
45	chr4:175214600-175241600	Weak transcription	Thymus	Thymus
46	chr4:175214600-175241800	Weak transcription	Pancreas	Pancrea
47	chr4:175214600-175242000	Weak transcription	Brain Substantia Nigra	brain
48	chr4:175214600-175243200	Weak transcription	Ovary	ovary
49	chr4:175214600-175244800	Weak transcription	Psoas Muscle	Psoas
50	chr4:175214600-175245400	Weak transcription	HSMM	muscle

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