Variant report

Variant	rs12252274
Chromosome Location	chr10:6139397-6139398
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	chr10:6137316..6139736-chr10:6243153..6245060,3	MCF-7	breast:
2	chr10:6130789..6132928-chr10:6134999..6139816,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213994	Chromatin interaction
ENSG00000170525	Chromatin interaction
ENSG00000134453	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10905861	0.84[ASN][1000 genomes]
rs11256626	0.88[ASN][1000 genomes]
rs11256664	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11256685	1.00[ASN][1000 genomes]
rs11256761	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11256763	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11256801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256810	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11256854	0.92[ASN][1000 genomes]
rs11256895	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12254328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12262454	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12263912	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12264240	1.00[ASN][1000 genomes]
rs12412910	0.88[ASN][1000 genomes]
rs12416306	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3750669	0.89[ASN][1000 genomes]
rs58138632	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59330649	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60859211	1.00[ASN][1000 genomes]
rs60960627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	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	chr10:6132400-6139600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:6132800-6139400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr10:6132800-6139600	Weak transcription	NH-A	brain
4	chr10:6132800-6143200	Weak transcription	HSMMtube	muscle
5	chr10:6132800-6145600	Weak transcription	Fetal Kidney	kidney
6	chr10:6132800-6150400	Weak transcription	Stomach Mucosa	stomach
7	chr10:6132800-6152000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:6133800-6139400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr10:6133800-6139600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr10:6133800-6149000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr10:6134000-6139600	Weak transcription	HMEC	breast
12	chr10:6134000-6142400	Weak transcription	Hela-S3	cervix
13	chr10:6134000-6149800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr10:6134800-6142200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr10:6136200-6141000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr10:6136600-6139600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr10:6136800-6150600	Strong transcription	Fetal Thymus	thymus
18	chr10:6137400-6139600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr10:6137400-6140800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr10:6137400-6145200	Strong transcription	Fetal Intestine Small	intestine
21	chr10:6137400-6150600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr10:6137400-6158600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr10:6137800-6139600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr10:6137800-6144200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr10:6137800-6144600	Strong transcription	K562	blood
26	chr10:6137800-6150400	Strong transcription	Primary B cells from cord blood	blood
27	chr10:6138000-6142000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr10:6138000-6143600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr10:6138000-6159400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr10:6138200-6139600	Weak transcription	HSMM	muscle
31	chr10:6138200-6139800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr10:6138200-6140200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr10:6138200-6140400	Strong transcription	HepG2	liver
34	chr10:6138200-6146000	Strong transcription	Thymus	Thymus
35	chr10:6138200-6150400	Strong transcription	Primary T cells from cord blood	blood
36	chr10:6138200-6150800	Strong transcription	Dnd41	blood
37	chr10:6138200-6159200	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr10:6138400-6139800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr10:6138400-6139800	Weak transcription	GM12878-XiMat	blood
40	chr10:6138400-6143200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr10:6138400-6143400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr10:6138400-6144200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr10:6138400-6145600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr10:6138400-6145800	Weak transcription	Psoas Muscle	Psoas
45	chr10:6138400-6146800	Weak transcription	Ovary	ovary
46	chr10:6138400-6150200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr10:6138400-6150400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr10:6138400-6150600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr10:6138400-6151000	Weak transcription	Fetal Heart	heart
50	chr10:6138400-6152200	Weak transcription	Fetal Brain Male	brain

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