Variant report

Variant	rs10565
Chromosome Location	chr4:175241128-175241129
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:175143195..175144498-chr4:175239947..175241349,5	MCF-7	breast:
2	chr4:175201466..175203946-chr4:175240301..175242969,2	K562	blood:
3	chr4:175201466..175204098-chr4:175240301..175242969,3	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10034021	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10520275	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11929798	1.00[CHB][hapmap]
rs11933187	1.00[CHB][hapmap]
rs11939946	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11940726	0.88[ASN][1000 genomes]
rs11940758	0.88[ASN][1000 genomes]
rs11942947	1.00[CHB][hapmap]
rs11944262	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11946084	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13101580	1.00[CHB][hapmap]
rs13128257	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13130276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17291087	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17291128	1.00[CEU][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17291408	1.00[CEU][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2332836	0.82[CEU][hapmap]
rs34988464	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35918158	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs41279509	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4287982	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695915	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4695919	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs4695922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695923	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6553777	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs68084371	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6824643	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6851312	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72702217	0.81[EUR][1000 genomes]
rs7661236	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7669484	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][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	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
4	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10565	CEP44	cis	Thyroid	GTEx
rs10565	KIAA1712	cis	multi-tissue	Pritchard

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175205600-175241600	Weak transcription	Small Intestine	intestine
2	chr4:175206800-175241800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:175207000-175242000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr4:175214600-175241600	Weak transcription	Lung	lung
5	chr4:175214600-175241600	Weak transcription	Thymus	Thymus
6	chr4:175214600-175241800	Weak transcription	Pancreas	Pancrea
7	chr4:175214600-175242000	Weak transcription	Brain Substantia Nigra	brain
8	chr4:175214600-175243200	Weak transcription	Ovary	ovary
9	chr4:175214600-175244800	Weak transcription	Psoas Muscle	Psoas
10	chr4:175214600-175245400	Weak transcription	HSMM	muscle
11	chr4:175214600-175254800	Weak transcription	Esophagus	oesophagus
12	chr4:175214800-175241200	Weak transcription	Brain Anterior Caudate	brain
13	chr4:175215200-175241600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:175215200-175242600	Weak transcription	GM12878-XiMat	blood
15	chr4:175217600-175241600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr4:175218600-175242000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:175219000-175242800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr4:175222400-175242000	Weak transcription	Fetal Intestine Small	intestine
19	chr4:175222600-175241400	Weak transcription	Spleen	Spleen
20	chr4:175225400-175241800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr4:175225800-175241600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr4:175230000-175245800	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:175230600-175241600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:175230600-175242800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr4:175230800-175246200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:175231800-175243200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:175232400-175247000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:175233800-175252600	Weak transcription	Left Ventricle	heart
29	chr4:175233800-175255800	Weak transcription	Fetal Intestine Large	intestine
30	chr4:175234000-175241800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr4:175234200-175241200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:175234600-175241600	Weak transcription	Fetal Lung	lung
33	chr4:175236200-175242800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:175236200-175258400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:175236400-175245400	Weak transcription	NHDF-Ad	bronchial
36	chr4:175236600-175242600	Weak transcription	A549	lung
37	chr4:175237200-175241400	Strong transcription	Fetal Thymus	thymus
38	chr4:175237200-175242000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:175237200-175242400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr4:175237400-175241200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr4:175237400-175241800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr4:175237400-175242000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr4:175237800-175245600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:175238000-175241800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:175238000-175242800	Weak transcription	Placenta	Placenta
46	chr4:175238000-175243000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr4:175238000-175243400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr4:175238000-175243400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr4:175238000-175244800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr4:175238000-175254800	Weak transcription	Adipose Nuclei	Adipose

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