Variant report

Variant	rs2329489
Chromosome Location	chr7:50768153-50768154
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1014384	0.80[JPT][hapmap]
rs1019000	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1024531	0.88[ASN][1000 genomes]
rs10265504	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10486761	0.85[JPT][hapmap]
rs11238297	0.82[ASN][1000 genomes]
rs11238326	0.80[JPT][hapmap]
rs11238337	0.80[JPT][hapmap]
rs11763072	0.95[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11763778	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11765762	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11983539	0.80[JPT][hapmap]
rs12668316	0.91[ASN][1000 genomes]
rs13311390	0.95[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2058014	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074777	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2108349	0.82[ASN][1000 genomes]
rs2190502	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214963	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237490	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2299153	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3779072	0.83[ASW][hapmap];0.87[MKK][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs3801000	0.87[ASN][1000 genomes]
rs4521715	0.89[CEU][hapmap];0.93[CHB][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4947806	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6593164	0.85[JPT][hapmap]
rs6593174	0.80[JPT][hapmap]
rs6943153	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6943901	0.80[JPT][hapmap]
rs6963498	0.80[JPT][hapmap]
rs6967612	0.90[ASN][1000 genomes]
rs6971834	0.80[JPT][hapmap]
rs6979369	0.84[JPT][hapmap]
rs757773	0.85[JPT][hapmap]
rs757774	0.84[JPT][hapmap]
rs7793570	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs7809623	0.90[ASN][1000 genomes]
rs7809775	0.85[ASN][1000 genomes]
rs933360	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1032882	chr7:50611138-50775257	Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv538834	chr7:50611138-50775257	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv1031138	chr7:50651793-50814881	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2329489	PTK2	trans	lymphoblastoid	seeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50742600-50792000	Weak transcription	Primary T cells from cord blood	blood
2	chr7:50745800-50769600	Weak transcription	Gastric	stomach
3	chr7:50750000-50778600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:50753800-50770000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr7:50755400-50777000	Weak transcription	Esophagus	oesophagus
6	chr7:50755600-50768400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr7:50755800-50768400	Weak transcription	A549	lung
8	chr7:50756200-50770000	Weak transcription	NHDF-Ad	bronchial
9	chr7:50756200-50779200	Weak transcription	Osteobl	bone
10	chr7:50756400-50769800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr7:50756400-50769800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:50757000-50771400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:50757000-50775000	Weak transcription	Psoas Muscle	Psoas
14	chr7:50757400-50771200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:50757400-50772600	Weak transcription	Aorta	Aorta
16	chr7:50757600-50768200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:50757600-50768400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr7:50758800-50771600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr7:50758800-50779400	Weak transcription	Fetal Kidney	kidney
20	chr7:50759200-50768200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:50759200-50769800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr7:50761600-50769600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr7:50761600-50771200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr7:50761600-50771600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:50761800-50769000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:50761800-50771200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr7:50762000-50769400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr7:50762000-50769400	Weak transcription	Placenta	Placenta
29	chr7:50762000-50769600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr7:50762000-50771400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr7:50762000-50772400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr7:50762200-50768200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr7:50762200-50772800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr7:50762400-50768800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr7:50762400-50769000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr7:50762800-50769800	Weak transcription	Right Ventricle	heart
37	chr7:50763000-50768600	Weak transcription	Hela-S3	cervix
38	chr7:50763200-50769000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:50763200-50769400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr7:50763400-50769000	Weak transcription	Left Ventricle	heart
41	chr7:50763400-50806800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr7:50764000-50778800	Weak transcription	HSMM	muscle
43	chr7:50765400-50768400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:50765400-50776800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr7:50765600-50769000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr7:50765600-50769000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr7:50765600-50769000	Weak transcription	Spleen	Spleen
48	chr7:50765600-50769600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr7:50765600-50770000	Weak transcription	HUVEC	blood vessel
50	chr7:50765600-50771400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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