Variant report

Variant	rs12254328
Chromosome Location	chr10:6140340-6140341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:6139421..6141396-chr10:6148385..6149953,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10905861	0.80[ASN][1000 genomes]
rs11256626	0.84[ASN][1000 genomes]
rs11256664	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11256685	0.96[ASN][1000 genomes]
rs11256761	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11256763	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11256801	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11256810	1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11256854	0.88[ASN][1000 genomes]
rs11256895	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12252274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12262454	1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12263912	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12264240	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs12412910	0.84[ASN][1000 genomes]
rs12416306	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3750669	0.85[ASN][1000 genomes]
rs58138632	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59330649	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60859211	0.96[ASN][1000 genomes]
rs60960627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6602450	1.00[YRI][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	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv894815	chr10:6108439-6161781	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1040397	chr10:6129759-6158697	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6132800-6143200	Weak transcription	HSMMtube	muscle
2	chr10:6132800-6145600	Weak transcription	Fetal Kidney	kidney
3	chr10:6132800-6150400	Weak transcription	Stomach Mucosa	stomach
4	chr10:6132800-6152000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:6133800-6149000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr10:6134000-6142400	Weak transcription	Hela-S3	cervix
7	chr10:6134000-6149800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr10:6134800-6142200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr10:6136200-6141000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr10:6136800-6150600	Strong transcription	Fetal Thymus	thymus
11	chr10:6137400-6140800	Enhancers	H1 Cell Line	embryonic stem cell
12	chr10:6137400-6145200	Strong transcription	Fetal Intestine Small	intestine
13	chr10:6137400-6150600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr10:6137400-6158600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr10:6137800-6144200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr10:6137800-6144600	Strong transcription	K562	blood
17	chr10:6137800-6150400	Strong transcription	Primary B cells from cord blood	blood
18	chr10:6138000-6142000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr10:6138000-6143600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr10:6138000-6159400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr10:6138200-6140400	Strong transcription	HepG2	liver
22	chr10:6138200-6146000	Strong transcription	Thymus	Thymus
23	chr10:6138200-6150400	Strong transcription	Primary T cells from cord blood	blood
24	chr10:6138200-6150800	Strong transcription	Dnd41	blood
25	chr10:6138200-6159200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr10:6138400-6143200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr10:6138400-6143400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr10:6138400-6144200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr10:6138400-6145600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr10:6138400-6145800	Weak transcription	Psoas Muscle	Psoas
31	chr10:6138400-6146800	Weak transcription	Ovary	ovary
32	chr10:6138400-6150200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr10:6138400-6150400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr10:6138400-6150600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr10:6138400-6151000	Weak transcription	Fetal Heart	heart
36	chr10:6138400-6152200	Weak transcription	Fetal Brain Male	brain
37	chr10:6138400-6154000	Weak transcription	Small Intestine	intestine
38	chr10:6138600-6144200	Weak transcription	Fetal Brain Female	brain
39	chr10:6138600-6145600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr10:6138800-6150200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr10:6138800-6150400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr10:6138800-6150600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr10:6138800-6152800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr10:6138800-6159200	Strong transcription	Placenta	Placenta
45	chr10:6138800-6159400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr10:6139000-6140400	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr10:6139000-6140400	Strong transcription	Brain Angular Gyrus	brain
48	chr10:6139000-6140400	Strong transcription	Brain Anterior Caudate	brain
49	chr10:6139000-6140400	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr10:6139000-6140400	Strong transcription	NHDF-Ad	bronchial

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