Variant report

Variant	rs2788868
Chromosome Location	chr7:86568521-86568522
allele	A/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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:86568193..86568776-chr7:87081301..87082150,2	MCF-7	breast:
2	chr7:86567674..86570136-chr7:86576947..86578810,2	K562	blood:
3	chr7:86567936..86568762-chr7:86865574..86866888,3	K562	blood:
4	chr7:86566998..86572829-chr7:86779731..86785521,7	MCF-7	breast:
5	chr7:86566315..86569287-chr7:86782697..86785356,2	K562	blood:
6	chr7:86566997..86568665-chr7:86776985..86778499,2	MCF-7	breast:
7	chr7:86565014..86570246-chr7:86776196..86779277,4	K562	blood:
8	chr7:86568242..86569711-chr7:86777392..86778327,7	MCF-7	breast:
9	chr7:86566956..86570257-chr7:86571660..86574220,4	K562	blood:
10	chr7:86568474..86569016-chr7:86687689..86688565,2	MCF-7	breast:
11	chr7:86567223..86569708-chr7:86571997..86573517,2	MCF-7	breast:
12	chr7:86567664..86570566-chr7:86835025..86837514,2	K562	blood:
13	chr7:86568296..86569388-chr7:86777465..86778298,4	MCF-7	breast:
14	chr7:86568259..86569226-chr7:86776924..86778150,7	K562	blood:
15	chr7:86567168..86569844-chr7:86780839..86782755,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000135164	Chromatin interaction
ENSG00000224046	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10235954	0.99[ASN][1000 genomes]
rs10267763	1.00[CHB][hapmap]
rs11976876	1.00[CHB][hapmap]
rs11979332	1.00[CHB][hapmap]
rs12704298	0.88[ASN][1000 genomes]
rs12704299	1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]
rs1557665	1.00[CHB][hapmap]
rs17126	0.82[GIH][hapmap]
rs1767721	0.88[CEU][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs17697878	1.00[CHB][hapmap]
rs17697894	1.00[CHB][hapmap]
rs17765493	1.00[CHB][hapmap]
rs2373361	0.85[CHB][hapmap]
rs2519713	0.83[GIH][hapmap]
rs6965383	1.00[JPT][hapmap]
rs7781178	1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs7807203	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025032	chr7:86032479-86642973	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv532147	chr7:86299225-87121975	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv1015870	chr7:86490491-86802320	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
6	nsv539000	chr7:86490491-86802320	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
7	nsv527889	chr7:86496042-86832603	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2788868	CDK14	cis	cerebellum	SCAN
rs2788868	SEMA3D	cis	cerebellum	SCAN
rs2788868	C7orf62	cis	cerebellum	SCAN
rs2788868	DMTF1	cis	cerebellum	SCAN
rs2788868	STEAP4	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86498400-86576200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:86518000-86568800	Weak transcription	Psoas Muscle	Psoas
3	chr7:86518000-86577000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:86521000-86576400	Weak transcription	Hela-S3	cervix
5	chr7:86527000-86577000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:86527200-86575800	Weak transcription	Left Ventricle	heart
7	chr7:86531200-86568800	Weak transcription	Brain Angular Gyrus	brain
8	chr7:86539200-86578800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:86541600-86568800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr7:86543200-86568800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr7:86543400-86571400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:86551000-86576200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr7:86554800-86568800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr7:86555000-86577000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr7:86561000-86568800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:86561600-86568800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr7:86561800-86578600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:86562200-86572800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:86563000-86578200	Weak transcription	HUVEC	blood vessel
20	chr7:86563200-86568800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr7:86563200-86568800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:86564400-86572400	Weak transcription	Fetal Heart	heart
23	chr7:86565600-86568800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr7:86565600-86569400	Strong transcription	K562	blood
25	chr7:86565800-86568800	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr7:86565800-86569000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:86565800-86569000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr7:86566000-86568800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr7:86566000-86568800	Weak transcription	Brain Substantia Nigra	brain
30	chr7:86566400-86568800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr7:86567200-86570600	Weak transcription	Adipose Nuclei	Adipose
32	chr7:86567400-86568600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr7:86567400-86568800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr7:86567400-86568800	Weak transcription	Brain Anterior Caudate	brain
35	chr7:86567600-86568600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr7:86567600-86570600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr7:86567600-86578600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:86567800-86576400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr7:86568200-86576200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr7:86568400-86569800	Enhancers	Brain Hippocampus Middle	brain
41	chr7:86568400-86571200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:86568400-86576000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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