Variant report

Variant	rs10520275
Chromosome Location	chr4:175182577-175182578
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:175182462..175186203-chr4:175202601..175205793,3	MCF-7	breast:
2	chr4:175172359..175176044-chr4:175180027..175182718,3	K562	blood:
3	chr4:175182024..175184066-chr4:175201212..175203528,2	K562	blood:
4	chr4:175181006..175183823-chr4:175186076..175188639,2	K562	blood:
5	chr4:175181041..175183420-chr4:175187913..175190511,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164117	Chromatin interaction
ENSG00000164118	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10034021	1.00[CEU][hapmap]
rs10565	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11939946	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11944262	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs11946084	0.89[CEU][hapmap]
rs13128257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13130276	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1508222	0.86[ASN][1000 genomes]
rs17291087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17291128	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17291408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17357120	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2332836	0.82[CEU][hapmap]
rs41279509	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4287982	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs4695915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695922	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6553777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68084371	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6824643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6851312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72702217	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7661236	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10520275	KIAA1712	cis	multi-tissue	Pritchard
rs10520275	CEP44	cis	Thyroid	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175147600-175195200	Weak transcription	Psoas Muscle	Psoas
2	chr4:175151400-175192800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:175153200-175184000	Weak transcription	Lung	lung
4	chr4:175153400-175191600	Weak transcription	Fetal Muscle Leg	muscle
5	chr4:175154200-175204000	Weak transcription	Aorta	Aorta
6	chr4:175154200-175204200	Weak transcription	Esophagus	oesophagus
7	chr4:175154400-175186200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:175154400-175202400	Weak transcription	Gastric	stomach
9	chr4:175155400-175185000	Weak transcription	Spleen	Spleen
10	chr4:175155800-175186600	Weak transcription	Fetal Brain Female	brain
11	chr4:175156800-175183400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:175157000-175184000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr4:175158800-175202000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:175159000-175184000	Weak transcription	Ovary	ovary
15	chr4:175159000-175184200	Weak transcription	Fetal Lung	lung
16	chr4:175159800-175199800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:175161000-175192400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr4:175169800-175203600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:175171800-175195200	Weak transcription	Pancreas	Pancrea
20	chr4:175173800-175185000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:175174000-175188000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:175174600-175184200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:175174800-175186600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr4:175174800-175199800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr4:175174800-175203400	Weak transcription	Thymus	Thymus
26	chr4:175175000-175196200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr4:175175000-175198600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr4:175175200-175183400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr4:175177200-175188000	Weak transcription	HMEC	breast
30	chr4:175177400-175183800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:175177400-175183800	Weak transcription	Fetal Stomach	stomach
32	chr4:175177400-175184600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr4:175177400-175187200	Weak transcription	Brain Germinal Matrix	brain
34	chr4:175177400-175189000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:175177400-175190400	Weak transcription	Fetal Kidney	kidney
36	chr4:175177400-175197800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr4:175177600-175192000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:175178000-175183400	Weak transcription	HSMM	muscle
39	chr4:175178000-175189200	Weak transcription	Fetal Heart	heart
40	chr4:175178000-175198600	Weak transcription	K562	blood
41	chr4:175178000-175203600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr4:175178200-175185400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:175178200-175191400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:175178200-175193800	Weak transcription	HSMMtube	muscle
45	chr4:175178800-175187600	Weak transcription	Primary B cells from cord blood	blood
46	chr4:175179000-175184000	Weak transcription	Adipose Nuclei	Adipose
47	chr4:175179200-175183800	Weak transcription	Primary T cells from cord blood	blood
48	chr4:175179200-175184000	Weak transcription	Left Ventricle	heart
49	chr4:175179200-175185800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:175179200-175192200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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