Variant report

Variant	rs12660319
Chromosome Location	chr6:24404862-24404863
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24402909..24405943-chr6:24492830..24496087,3	K562	blood:
2	chr6:24401784..24404907-chr6:24494976..24497958,4	MCF-7	breast:
3	chr6:24404630..24407333-chr6:24559685..24561436,2	K562	blood:

Variant related genes	Relation type
ENSG00000112294	Chromatin interaction
ENSG00000112293	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10498720	1.00[CEU][hapmap]
rs12661981	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[EUR][1000 genomes]
rs12665371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16889286	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.90[EUR][1000 genomes]
rs1772254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs2295651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761790	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs41271783	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61733147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793713	0.82[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	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24401800-24405400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:24402400-24406600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr6:24402600-24405000	Active TSS	H1 Cell Line	embryonic stem cell
4	chr6:24402600-24405200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:24402600-24405400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr6:24402600-24405600	Active TSS	GM12878-XiMat	blood
7	chr6:24402800-24405400	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:24402800-24405400	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:24402800-24405800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:24403000-24405000	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr6:24403000-24405400	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr6:24403800-24405200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:24404000-24405400	Weak transcription	Esophagus	oesophagus
14	chr6:24404000-24406000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
15	chr6:24404000-24406600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:24404000-24408000	Weak transcription	Aorta	Aorta
17	chr6:24404000-24408000	Weak transcription	Lung	lung
18	chr6:24404000-24408000	Weak transcription	Spleen	Spleen
19	chr6:24404000-24408800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:24404000-24413000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:24404200-24405000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr6:24404200-24405000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr6:24404200-24405400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr6:24404200-24405400	Weak transcription	Pancreas	Pancrea
25	chr6:24404200-24413000	Weak transcription	Gastric	stomach
26	chr6:24404400-24405000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:24404400-24405000	Transcr. at gene 5' and 3'	A549	lung
28	chr6:24404400-24405000	Transcr. at gene 5' and 3'	NHEK	skin
29	chr6:24404400-24405200	Flanking Active TSS	HepG2	liver
30	chr6:24404400-24405400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:24404400-24407600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:24404400-24412000	Weak transcription	Colonic Mucosa	Colon
33	chr6:24404400-24412400	Weak transcription	Fetal Brain Male	brain
34	chr6:24404400-24412800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:24404400-24412800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr6:24404400-24413000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:24404600-24405000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:24404600-24405000	Enhancers	Primary T cells from cord blood	blood
39	chr6:24404600-24405000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr6:24404600-24405000	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr6:24404600-24405000	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr6:24404600-24405200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:24404600-24405200	Enhancers	Brain Germinal Matrix	brain
44	chr6:24404600-24405200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:24404600-24405200	Enhancers	Fetal Brain Female	brain
46	chr6:24404600-24405400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:24404600-24405400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:24404600-24405400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr6:24404600-24405400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr6:24404600-24405400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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