Variant report

Variant	rs666462
Chromosome Location	chr6:44205027-44205028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:44123357..44125146-chr6:44203946..44206894,2	K562	blood:
2	chr6:44139023..44142178-chr6:44202710..44207835,5	K562	blood:
3	chr6:44077806..44078726-chr6:44204971..44206412,5	MCF-7	breast:
4	chr6:44137717..44140173-chr6:44201270..44205583,3	MCF-7	breast:
5	chr6:44077806..44078726-chr6:44204971..44206412,4	MCF-7	breast:
6	chr6:44079762..44081284-chr6:44204790..44206941,2	K562	blood:
7	chr6:44120961..44123352-chr6:44203847..44206405,2	MCF-7	breast:
8	chr6:44199025..44201599-chr6:44203689..44206993,5	MCF-7	breast:
9	chr6:44194591..44197466-chr6:44204314..44205838,2	MCF-7	breast:
10	chr6:44094095..44096990-chr6:44204419..44207697,4	MCF-7	breast:
11	chr6:44052482..44055153-chr6:44202831..44205817,2	K562	blood:
12	chr6:44093264..44095446-chr6:44204345..44207044,2	K562	blood:
13	chr6:44188998..44189909-chr6:44204941..44206651,4	K562	blood:
14	chr6:44051124..44053637-chr6:44204273..44206013,2	MCF-7	breast:
15	chr6:44184911..44192138-chr6:44201380..44207306,8	MCF-7	breast:
16	chr6:44118511..44121325-chr6:44203702..44206845,3	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC29A1-2	chr6:44204713-44208319	NONHSAT112955

No data

Variant related genes	Relation type
ENSG00000137216	Chromatin interaction
ENSG00000112759	Chromatin interaction
ENSG00000180992	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2070695	0.90[ASN][1000 genomes]
rs2894567	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3734704	0.99[ASN][1000 genomes]
rs495061	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760370	0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs9367189	0.97[ASN][1000 genomes]
rs9367190	0.84[CHB][hapmap]
rs9381298	0.84[ASN][1000 genomes]
rs9381299	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9381303	0.84[CHB][hapmap]
rs9394992	0.88[CHD][hapmap]
rs9394994	0.84[ASN][1000 genomes]
rs9394995	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS 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	201 gene(s)	inside rSNPs	diseases
2	nsv885851	chr6:44178471-44240559	Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
3	nsv885852	chr6:44185901-44222718	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv603003	chr6:44191920-44253765	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
5	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
7	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv524398	chr6:44200953-44253765	Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	nsv981326	chr6:44201100-44205684	Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs666462	PTK7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44199800-44205200	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr6:44203000-44205200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:44203000-44205200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:44203000-44205200	Weak transcription	Primary T cells from cord blood	blood
5	chr6:44203000-44205400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:44203200-44205200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:44203200-44205200	Weak transcription	Fetal Brain Female	brain
8	chr6:44203200-44205200	Weak transcription	Ovary	ovary
9	chr6:44203400-44205200	Weak transcription	Fetal Brain Male	brain
10	chr6:44203600-44205200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:44204400-44205400	Enhancers	Pancreas	Pancrea
12	chr6:44204600-44205200	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr6:44204600-44205200	Enhancers	Fetal Muscle Trunk	muscle
14	chr6:44204600-44205400	Flanking Active TSS	Hela-S3	cervix
15	chr6:44204600-44207400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:44204800-44205200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:44204800-44205200	Enhancers	Primary B cells from cord blood	blood
18	chr6:44204800-44205200	Enhancers	Primary B cells from peripheral blood	blood
19	chr6:44204800-44205200	Enhancers	Primary hematopoietic stem cells	blood
20	chr6:44204800-44205200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr6:44204800-44205200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr6:44204800-44205200	Enhancers	Brain Angular Gyrus	brain
23	chr6:44204800-44205200	Enhancers	NH-A	brain
24	chr6:44204800-44205400	Flanking Active TSS	Liver	Liver
25	chr6:44204800-44205400	Enhancers	Placenta	Placenta
26	chr6:44204800-44205400	Enhancers	Left Ventricle	heart
27	chr6:44204800-44205400	Enhancers	Placenta Amnion	Placenta Amnion
28	chr6:44204800-44205400	Flanking Active TSS	Rectal Smooth Muscle	rectum
29	chr6:44204800-44205400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr6:44204800-44205400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr6:44204800-44205400	Flanking Active TSS	HepG2	liver
32	chr6:44204800-44205400	Flanking Active TSS	HSMMtube	muscle
33	chr6:44204800-44205800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:44204800-44205800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:44204800-44206000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr6:44204800-44206200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:44204800-44206200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:44204800-44206200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:44204800-44206200	Flanking Active TSS	Osteobl	bone
40	chr6:44205000-44205200	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:44205000-44205200	Enhancers	H9 Cell Line	embryonic stem cell
42	chr6:44205000-44205200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:44205000-44205200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:44205000-44205200	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr6:44205000-44205200	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr6:44205000-44205200	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr6:44205000-44205200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr6:44205000-44205200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:44205000-44205200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:44205000-44205200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast

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