Variant report

Variant	rs9919407
Chromosome Location	chr10:52378044-52378045
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52315813..52318278-chr10:52376288..52379260,2	K562	blood:
2	chr10:52349124..52352049-chr10:52377946..52381102,3	K562	blood:
3	chr10:52355970..52358426-chr10:52377071..52379971,2	K562	blood:
4	chr10:52346092..52348176-chr10:52375554..52378162,2	K562	blood:

Variant related genes	Relation type
ENSG00000238523	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10160082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11006407	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11006510	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11006513	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11006527	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12247712	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12247977	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12248247	0.84[AFR][1000 genomes]
rs12248669	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12248873	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12249902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12250028	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12260665	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12260996	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12261261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12265805	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16906634	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9919374	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52365400-52379400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr10:52365800-52378200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr10:52366000-52381600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr10:52367200-52379400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr10:52367400-52381400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr10:52367600-52378400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr10:52367600-52381400	Weak transcription	NHLF	lung
8	chr10:52367600-52381400	Weak transcription	Osteobl	bone
9	chr10:52369000-52378800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr10:52370200-52378400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr10:52370800-52378400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr10:52371000-52381200	Weak transcription	Fetal Stomach	stomach
13	chr10:52371200-52378200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr10:52371200-52381600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr10:52371800-52378400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr10:52372600-52381600	Weak transcription	Aorta	Aorta
17	chr10:52372800-52379200	Weak transcription	Fetal Brain Male	brain
18	chr10:52373000-52380600	Weak transcription	Fetal Intestine Small	intestine
19	chr10:52373200-52378400	Weak transcription	Brain Germinal Matrix	brain
20	chr10:52373200-52380600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr10:52373400-52378800	Weak transcription	Gastric	stomach
22	chr10:52374000-52378200	Weak transcription	Fetal Kidney	kidney
23	chr10:52374200-52378600	Weak transcription	Fetal Lung	lung
24	chr10:52374200-52381200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr10:52374400-52378400	Weak transcription	Brain Substantia Nigra	brain
26	chr10:52374400-52380600	Weak transcription	Fetal Intestine Large	intestine
27	chr10:52374400-52381200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr10:52374400-52381600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr10:52374400-52381600	Weak transcription	Spleen	Spleen
30	chr10:52374600-52378200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr10:52374600-52378400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr10:52374600-52378400	Weak transcription	Esophagus	oesophagus
33	chr10:52374600-52379800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr10:52374600-52380800	Weak transcription	Fetal Muscle Leg	muscle
35	chr10:52374600-52381600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr10:52374800-52378200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr10:52374800-52378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr10:52374800-52378600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr10:52374800-52380000	Weak transcription	HepG2	liver
40	chr10:52374800-52381600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr10:52375000-52378400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr10:52375000-52378400	Weak transcription	Fetal Thymus	thymus
43	chr10:52375000-52381600	Weak transcription	Ovary	ovary
44	chr10:52375000-52381600	Weak transcription	Stomach Mucosa	stomach
45	chr10:52375200-52378400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr10:52375200-52378600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr10:52375400-52378400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr10:52375400-52378400	Weak transcription	Brain Anterior Caudate	brain
49	chr10:52375400-52378400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr10:52375400-52378600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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