Variant report

Variant	rs3198123
Chromosome Location	chr2:55207693-55207694
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55204435..55209089-chr2:55274911..55278052,4	MCF-7	breast:
2	chr2:55205322..55208790-chr2:55211251..55214642,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10084445	1.00[YRI][hapmap]
rs10173203	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10189094	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs11125554	1.00[YRI][hapmap]
rs13385999	0.88[LWK][hapmap]
rs13387836	0.82[EUR][1000 genomes]
rs17046567	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs17046569	1.00[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs3806572	0.95[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6705519	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6757907	0.87[CEU][hapmap]
rs6760379	0.82[EUR][1000 genomes]
rs7584992	0.80[LWK][hapmap]
rs7601895	0.87[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3198123	HSS00293720	cis	multi-tissue	Pritchard
rs3198123	VRK2	cis	cerebellum	SCAN
rs3198123	TSPYL6	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55184800-55214800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:55191800-55211600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:55193400-55214800	Strong transcription	HepG2	liver
5	chr2:55193600-55214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:55193800-55211800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:55194000-55211800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:55195000-55215200	Strong transcription	Dnd41	blood
9	chr2:55195600-55210800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:55195800-55216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:55196200-55214600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
13	chr2:55196600-55208400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:55196600-55217200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:55196600-55217200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:55197800-55207800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr2:55198200-55212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:55198600-55215200	Weak transcription	Lung	lung
20	chr2:55198800-55215200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:55199200-55212400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:55199400-55208000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:55200200-55209600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:55200400-55213400	Weak transcription	Fetal Brain Male	brain
25	chr2:55200800-55208000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:55200800-55216600	Weak transcription	Colonic Mucosa	Colon
27	chr2:55201000-55208400	Weak transcription	Placenta	Placenta
28	chr2:55201200-55208000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr2:55201400-55208400	Weak transcription	Primary B cells from cord blood	blood
30	chr2:55202000-55207800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:55203800-55207800	Weak transcription	Psoas Muscle	Psoas
32	chr2:55203800-55207800	Weak transcription	HUVEC	blood vessel
33	chr2:55203800-55210000	Weak transcription	Ovary	ovary
34	chr2:55203800-55210800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:55203800-55222600	Weak transcription	Spleen	Spleen
36	chr2:55203800-55223800	Weak transcription	Pancreas	Pancrea
37	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
38	chr2:55204000-55208000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr2:55204000-55208800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:55204200-55208600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr2:55204200-55214800	Strong transcription	Fetal Thymus	thymus
42	chr2:55204400-55207800	Weak transcription	Brain Germinal Matrix	brain
43	chr2:55204400-55208600	Weak transcription	Primary T cells from cord blood	blood
44	chr2:55204600-55208400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:55204600-55209400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:55204600-55210600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr2:55204800-55208000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:55204800-55208200	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:55204800-55208200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:55204800-55210400	Strong transcription	Osteobl	bone

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