Variant report

Variant	rs2145635
Chromosome Location	chr14:97299853-97299854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:97271958..97274868-chr14:97298626..97301164,2	MCF-7	breast:
2	chr14:97299339..97301771-chr14:97302252..97306278,3	MCF-7	breast:
3	chr14:97293502..97295046-chr14:97299094..97301646,2	MCF-7	breast:
4	chr14:97293055..97295755-chr14:97296835..97300397,4	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10145383	1.00[CHB][hapmap]
rs10146571	0.90[CHB][hapmap]
rs11160369	0.91[CHB][hapmap]
rs11160377	0.92[ASN][1000 genomes]
rs11627455	0.92[ASN][1000 genomes]
rs11628733	0.91[CHB][hapmap]
rs12101203	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12433112	1.00[CHB][hapmap]
rs12586511	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12589919	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12590169	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12878184	1.00[CHB][hapmap]
rs12881995	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12882038	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12882853	0.90[CHB][hapmap]
rs12887093	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12889255	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12892609	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12893513	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12893711	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12894533	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12894621	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12897588	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17191471	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1957135	0.83[CHD][hapmap]
rs2145636	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2180897	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2224442	0.91[CHB][hapmap]
rs2224443	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2230532	1.00[CHB][hapmap]
rs4270096	1.00[CHB][hapmap]
rs4900346	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4900348	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4900350	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs4900351	0.90[CHB][hapmap]
rs4900352	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4900353	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4905548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4905549	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4905550	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4905551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4905558	0.81[CHB][hapmap]
rs4905561	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4905562	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4905563	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4905567	0.92[ASN][1000 genomes]
rs7156355	1.00[CHB][hapmap]
rs723810	1.00[CHB][hapmap]
rs736929	0.90[CHB][hapmap]
rs749279	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs764300	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8013081	1.00[CHB][hapmap]
rs8022152	0.92[ASN][1000 genomes]
rs9323955	1.00[CHB][hapmap];0.89[ASN][1000 genomes]

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	nsv1044202	chr14:97155291-97683983	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv542179	chr14:97155291-97683983	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv510650	chr14:97238489-97325221	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1052138	chr14:97271794-97322583	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv542180	chr14:97271794-97322583	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1043916	chr14:97275088-97320354	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1051182	chr14:97275088-97337039	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2145635	VRK1	cis	cerebellum	SCAN
rs2145635	VRK1	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:97264800-97321600	Weak transcription	Psoas Muscle	Psoas
2	chr14:97266200-97303200	Weak transcription	Hela-S3	cervix
3	chr14:97271600-97313800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr14:97282600-97300200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr14:97282800-97301800	Weak transcription	Thymus	Thymus
6	chr14:97283000-97300800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr14:97284600-97313800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr14:97287000-97301600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr14:97288200-97303200	Weak transcription	Brain Anterior Caudate	brain
10	chr14:97288200-97314400	Weak transcription	Lung	lung
11	chr14:97289400-97302000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr14:97291000-97326000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr14:97291200-97300000	Weak transcription	Adipose Nuclei	Adipose
14	chr14:97291200-97326200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr14:97291600-97302000	Weak transcription	NHLF	lung
16	chr14:97292800-97300800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr14:97293000-97300000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr14:97293000-97309000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr14:97293400-97300000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr14:97293400-97313800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr14:97293400-97326400	Weak transcription	Fetal Stomach	stomach
22	chr14:97293600-97300000	Weak transcription	A549	lung
23	chr14:97293600-97306200	Weak transcription	Colon Smooth Muscle	Colon
24	chr14:97293600-97323400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr14:97293800-97300000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr14:97293800-97313800	Weak transcription	Fetal Lung	lung
27	chr14:97294000-97300400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr14:97294000-97301000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr14:97294000-97314400	Weak transcription	Esophagus	oesophagus
30	chr14:97294000-97323000	Weak transcription	Gastric	stomach
31	chr14:97294000-97362600	Weak transcription	Spleen	Spleen
32	chr14:97294600-97313800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr14:97294800-97300800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr14:97296000-97307200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr14:97296200-97318400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr14:97296400-97300000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr14:97296400-97300200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr14:97296600-97302000	Weak transcription	HepG2	liver
39	chr14:97296800-97303200	Weak transcription	HUVEC	blood vessel
40	chr14:97297400-97300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr14:97297400-97300200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr14:97297400-97301600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr14:97297400-97302600	Weak transcription	Fetal Muscle Leg	muscle
44	chr14:97297400-97323000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr14:97297400-97328000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr14:97297600-97304600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr14:97297600-97353400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr14:97297800-97302200	Weak transcription	Aorta	Aorta
49	chr14:97298000-97310400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr14:97298000-97313600	Weak transcription	Stomach Smooth Muscle	stomach

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