Variant report

Variant	rs12661501
Chromosome Location	chr6:128388724-128388725
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:128388700-128388850	HCPEpiC	choroid plexus:	n/a	n/a

Variant related genes	Relation type
PTPRK	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs4895829	1.00[GIH][hapmap]
rs4897242	1.00[GIH][hapmap]
rs4897243	1.00[GIH][hapmap]
rs7757761	1.00[GIH][hapmap]
rs9375546	1.00[GIH][hapmap]
rs9482858	1.00[GIH][hapmap]
rs9482860	1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv604643	chr6:128359362-128493991	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128289000-128431000	Weak transcription	Psoas Muscle	Psoas
2	chr6:128347000-128405200	Weak transcription	Lung	lung
3	chr6:128350000-128401000	Weak transcription	Small Intestine	intestine
4	chr6:128367600-128398000	Weak transcription	HUVEC	blood vessel
5	chr6:128370000-128412600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:128372400-128412200	Weak transcription	Placenta	Placenta
7	chr6:128374600-128419400	Weak transcription	Esophagus	oesophagus
8	chr6:128375000-128419400	Weak transcription	Gastric	stomach
9	chr6:128375000-128433800	Weak transcription	Aorta	Aorta
10	chr6:128375600-128413000	Weak transcription	Colonic Mucosa	Colon
11	chr6:128377800-128403400	Weak transcription	Fetal Kidney	kidney
12	chr6:128378000-128390200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:128379000-128432800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:128379400-128390400	Weak transcription	NHDF-Ad	bronchial
15	chr6:128379400-128396600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:128379400-128412200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:128379600-128390000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:128379800-128389200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:128381800-128389200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:128383000-128389400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:128384000-128389600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr6:128384000-128396000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:128385000-128390800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:128385200-128388800	Enhancers	Brain Angular Gyrus	brain
25	chr6:128385400-128389000	Strong transcription	Fetal Thymus	thymus
26	chr6:128385600-128389000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:128385800-128406400	Weak transcription	Primary T cells from cord blood	blood
28	chr6:128385800-128419400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr6:128386400-128389600	Strong transcription	Duodenum Mucosa	Duodenum
30	chr6:128386600-128388800	Enhancers	Right Atrium	heart
31	chr6:128387000-128389000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr6:128387000-128389600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:128387200-128389000	Strong transcription	HSMM	muscle
34	chr6:128387200-128389400	Strong transcription	NH-A	brain
35	chr6:128387200-128389600	Strong transcription	Liver	Liver
36	chr6:128387400-128388800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:128387400-128389000	Strong transcription	Pancreas	Pancrea
38	chr6:128387400-128389600	Strong transcription	Fetal Stomach	stomach
39	chr6:128387400-128389600	Strong transcription	Ovary	ovary
40	chr6:128387600-128389600	Strong transcription	Fetal Intestine Large	intestine
41	chr6:128387600-128389600	Strong transcription	HepG2	liver
42	chr6:128387600-128390200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:128387800-128388800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr6:128387800-128389000	Strong transcription	Osteobl	bone
45	chr6:128388000-128388800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:128388000-128388800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:128388000-128388800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:128388000-128388800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:128388000-128388800	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr6:128388000-128388800	Flanking Active TSS	Brain Hippocampus Middle	brain

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