Variant report

Variant	rs6465836
Chromosome Location	chr7:101545685-101545686
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:101509122..101511427-chr7:101544764..101546984,2	K562	blood:
2	chr7:101497702..101501860-chr7:101544397..101548440,5	K562	blood:
3	chr7:101500144..101502029-chr7:101545108..101548084,3	K562	blood:
4	chr7:101527923..101529893-chr7:101545437..101547345,2	MCF-7	breast:
5	chr7:101535565..101538438-chr7:101544906..101547711,2	K562	blood:
6	chr7:101522402..101527695-chr7:101541882..101547914,5	MCF-7	breast:
7	chr7:101524859..101527642-chr7:101545155..101548859,4	K562	blood:
8	chr7:101544077..101549064-chr7:101550086..101553092,6	K562	blood:
9	chr7:101541658..101544389-chr7:101544721..101546512,2	K562	blood:
10	chr7:101545303..101548484-chr7:101553115..101557502,6	K562	blood:
11	chr7:101545055..101547008-chr7:101551122..101553066,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10229003	1.00[CHB][hapmap]
rs10245008	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs11768899	0.85[CHB][hapmap];0.91[CHD][hapmap]
rs11971810	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4236559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4729755	1.00[CHB][hapmap]
rs6957294	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6957361	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6961254	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6978555	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6979596	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7780749	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7803747	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv482846	chr7:101539981-101707666	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6465836	PDAP1	cis	cerebellum	SCAN
rs6465836	PVRIG	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101528600-101555200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:101529400-101554200	Weak transcription	Primary T cells from cord blood	blood
3	chr7:101530600-101559800	Weak transcription	GM12878-XiMat	blood
4	chr7:101531000-101548000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr7:101531400-101554600	Weak transcription	Hela-S3	cervix
6	chr7:101533800-101559000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:101534200-101546600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr7:101535400-101554400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:101535600-101554200	Weak transcription	HepG2	liver
10	chr7:101535600-101554600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr7:101535800-101555200	Weak transcription	Liver	Liver
12	chr7:101535800-101555600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr7:101537000-101547600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr7:101537000-101547600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr7:101537000-101554400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:101537000-101554600	Weak transcription	Fetal Intestine Large	intestine
17	chr7:101537600-101559000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr7:101539600-101548800	Weak transcription	Thymus	Thymus
19	chr7:101540000-101546400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr7:101540000-101555600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr7:101540200-101559200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr7:101540400-101548200	Weak transcription	Spleen	Spleen
23	chr7:101540400-101555200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:101540400-101559200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr7:101540600-101547200	Strong transcription	Fetal Intestine Small	intestine
26	chr7:101540800-101548600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr7:101541400-101554400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:101541400-101555000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr7:101541400-101555000	Weak transcription	Fetal Thymus	thymus
30	chr7:101541800-101548400	Weak transcription	Primary B cells from cord blood	blood
31	chr7:101542200-101546000	Enhancers	Fetal Heart	heart
32	chr7:101542400-101555600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr7:101542600-101558000	Weak transcription	Dnd41	blood
34	chr7:101543000-101546600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:101543600-101545800	Enhancers	Fetal Stomach	stomach
36	chr7:101543600-101546000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:101543600-101554400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr7:101543800-101545800	Enhancers	Rectal Smooth Muscle	rectum
39	chr7:101543800-101546800	Enhancers	Fetal Muscle Leg	muscle
40	chr7:101543800-101548600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr7:101544000-101545800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr7:101544000-101545800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr7:101544000-101546000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr7:101544000-101555200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr7:101544000-101558200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr7:101544000-101569800	Weak transcription	HMEC	breast
47	chr7:101544200-101545800	Enhancers	Right Atrium	heart
48	chr7:101544200-101546000	Enhancers	Psoas Muscle	Psoas
49	chr7:101544200-101554400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr7:101544200-101559200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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