Variant report

Variant	rs12205310
Chromosome Location	chr6:26605864-26605865
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26602910..26606507-chr6:26613473..26615906,4	K562	blood:
2	chr6:26604908..26609583-chr6:27112417..27116063,5	MCF-7	breast:
3	chr6:26603782..26606678-chr6:27060300..27062978,2	K562	blood:
4	chr6:26604919..26606656-chr6:27049423..27051797,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABT1-1	chr6:26604884-26606885	XLOC_005213

Variant related genes	Relation type
ENSG00000219770	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10456047	1.00[JPT][hapmap]
rs10456331	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10484441	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10946842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193283	1.00[JPT][hapmap]
rs12194036	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12208211	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12208272	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12211872	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12661560	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1884945	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2893857	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4712999	1.00[YRI][hapmap]
rs4713000	1.00[YRI][hapmap]
rs4713001	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4713011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap]
rs882010	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9393736	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12205310	ZSCAN23	cis	cerebellum	SCAN
rs12205310	HIST1H2BH	cis	cerebellum	SCAN
rs12205310	HIST1H4E	cis	cerebellum	SCAN
rs12205310	BTN2A1	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26598000-26606800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:26598200-26607800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:26599200-26607800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:26599200-26607800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:26599200-26607800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:26599400-26607800	Weak transcription	Fetal Intestine Small	intestine
7	chr6:26599600-26607800	Weak transcription	Colonic Mucosa	Colon
8	chr6:26599800-26607800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:26600000-26607800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr6:26600000-26607800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr6:26600000-26607800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:26600000-26607800	Weak transcription	Fetal Stomach	stomach
13	chr6:26600000-26607800	Weak transcription	Thymus	Thymus
14	chr6:26600000-26607800	Weak transcription	HepG2	liver
15	chr6:26600000-26607800	Weak transcription	NHLF	lung
16	chr6:26600000-26614000	Weak transcription	Spleen	Spleen
17	chr6:26600200-26607200	Weak transcription	Brain Germinal Matrix	brain
18	chr6:26600200-26607600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:26600200-26607600	Weak transcription	Hela-S3	cervix
20	chr6:26600200-26607800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr6:26600200-26607800	Weak transcription	Brain Angular Gyrus	brain
22	chr6:26600200-26607800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:26600200-26607800	Weak transcription	Fetal Kidney	kidney
24	chr6:26600200-26607800	Weak transcription	Dnd41	blood
25	chr6:26600200-26607800	Weak transcription	HMEC	breast
26	chr6:26600200-26607800	Weak transcription	Osteobl	bone
27	chr6:26600400-26607800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:26600400-26607800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:26600400-26607800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:26600400-26607800	Weak transcription	Liver	Liver
31	chr6:26600400-26607800	Weak transcription	Colon Smooth Muscle	Colon
32	chr6:26600400-26607800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr6:26600400-26607800	Weak transcription	Ovary	ovary
34	chr6:26600400-26607800	Weak transcription	A549	lung
35	chr6:26600400-26607800	Weak transcription	NHDF-Ad	bronchial
36	chr6:26600600-26607800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:26600600-26607800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:26600600-26607800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:26600600-26607800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr6:26600600-26607800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr6:26600600-26607800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:26600600-26607800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr6:26600800-26607000	Weak transcription	Fetal Brain Female	brain
44	chr6:26600800-26607600	Weak transcription	Brain Anterior Caudate	brain
45	chr6:26600800-26607600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr6:26600800-26607600	Weak transcription	Left Ventricle	heart
47	chr6:26600800-26607800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:26600800-26607800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr6:26600800-26607800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr6:26600800-26607800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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