Variant report

Variant	rs10412238
Chromosome Location	chr19:19318158-19318159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19317906-19318970	MCF-7	breast:	n/a	n/a
2	PAX5	chr19:19318140-19318524	GM12878	blood:	n/a	n/a
3	SUZ12	chr19:19318134-19318842	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19316331..19318362-chr19:19376972..19379894,2	K562	blood:
2	chr19:19316362..19318811-chr19:19332954..19335796,2	K562	blood:
3	chr19:19312779..19319489-chr19:19322201..19327588,8	K562	blood:
4	chr19:19316312..19318811-chr19:19331949..19335796,3	K562	blood:
5	chr19:19299448..19305567-chr19:19306959..19319217,21	K562	blood:
6	chr19:19314363..19315901-chr19:19317594..19320270,2	K562	blood:
7	chr19:19300744..19305499-chr19:19311426..19319217,10	K562	blood:
8	chr19:19317527..19320525-chr19:19340607..19343524,2	K562	blood:
9	chr19:19316640..19318564-chr19:19323281..19325590,2	MCF-7	breast:

No data

Variant related genes	Relation type
NR2C2AP	TF binding region
NCAN	TF binding region
ENSG00000254901	Chromatin interaction
ENSG00000213996	Chromatin interaction
ENSG00000064489	Chromatin interaction
ENSG00000213999	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000130287	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10401713	0.80[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10403193	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10409380	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10409894	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10424365	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1050483	0.90[CEU][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2283626	0.90[CEU][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28618105	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56007657	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7250569	0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73537466	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911304	chr19:19303802-19408164	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10412238	OCEL1	cis	cerebellum	SCAN
rs10412238	LRRC25	cis	parietal	SCAN
rs10412238	ZNF99	cis	parietal	SCAN
rs10412238	NCAN	cis	cerebellum	SCAN
rs10412238	FAM32A	cis	cerebellum	SCAN
rs10412238	FAM129C	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19314600-19318200	Weak transcription	Hela-S3	cervix
2	chr19:19314600-19318600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr19:19314600-19320600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr19:19314600-19322400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr19:19314800-19319000	Weak transcription	Brain Germinal Matrix	brain
6	chr19:19314800-19322200	Weak transcription	Fetal Brain Female	brain
7	chr19:19316800-19319000	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr19:19316800-19319000	Enhancers	Brain Anterior Caudate	brain
9	chr19:19317000-19318600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:19317200-19318400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr19:19317200-19318400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:19317200-19318800	Bivalent Enhancer	Brain Hippocampus Middle	brain
13	chr19:19317400-19319000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:19317400-19319000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr19:19317400-19319000	Bivalent Enhancer	Stomach Mucosa	stomach
16	chr19:19317400-19319200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr19:19317600-19318400	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr19:19317600-19319000	Enhancers	Spleen	Spleen
19	chr19:19317600-19319200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:19317800-19318400	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr19:19317800-19318800	Enhancers	Gastric	stomach
22	chr19:19317800-19318800	Enhancers	GM12878-XiMat	blood
23	chr19:19317800-19319000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr19:19317800-19319200	Enhancers	Primary B cells from peripheral blood	blood
25	chr19:19317800-19319200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:19317800-19319200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr19:19317800-19319200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:19317800-19319200	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr19:19318000-19318200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:19318000-19318400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr19:19318000-19318400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
32	chr19:19318000-19318600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:19318000-19318800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:19318000-19318800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
35	chr19:19318000-19319000	ZNF genes & repeats	Esophagus	oesophagus
36	chr19:19318000-19319000	Enhancers	K562	blood

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