Variant report

Variant	rs10420138
Chromosome Location	chr19:52704961-52704962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:52704607-52705072	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:52703908-52705233	GM12891	blood:	n/a	n/a
3	POLR2A	chr19:52703434-52705471	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:52704700-52704987	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr19:52704693-52705073	GM12892	blood:	n/a	n/a
6	POLR2A	chr19:52704613-52705213	GM12891	blood:	n/a	n/a
7	POLR2A	chr19:52703156-52705303	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:52704467-52706589	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:52703334-52705311	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:52703409-52705333	GM12892	blood:	n/a	n/a
11	POLR2A	chr19:52704626-52705335	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52692900..52696088-chr19:52702014..52707428,7	MCF-7	breast:

Variant related genes	Relation type
PPP2R1A	TF binding region
ENSG00000105568	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13346079	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786487	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4802901	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4802902	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802903	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802904	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509627	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111131	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[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	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10420138	ZNF347	cis	cerebellum	SCAN
rs10420138	RPL28	cis	cerebellum	SCAN
rs10420138	PPP1R12C	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52694400-52710200	ZNF genes & repeats	A549	lung
2	chr19:52694600-52732800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:52695200-52708400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:52695200-52711200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:52695400-52707600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:52695400-52732200	Strong transcription	Fetal Lung	lung
7	chr19:52695400-52733200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr19:52695600-52717400	Strong transcription	Primary hematopoietic stem cells	blood
9	chr19:52696000-52710800	Strong transcription	Thymus	Thymus
10	chr19:52696000-52723000	Strong transcription	Fetal Muscle Trunk	muscle
11	chr19:52696000-52732200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr19:52696000-52732400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:52696000-52733000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:52696200-52705200	Weak transcription	Small Intestine	intestine
15	chr19:52696200-52729200	Strong transcription	Fetal Intestine Large	intestine
16	chr19:52696200-52732400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr19:52696200-52732400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr19:52696200-52732400	Strong transcription	Primary B cells from cord blood	blood
19	chr19:52696800-52705600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr19:52697600-52732400	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr19:52697600-52733200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr19:52697800-52732200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:52697800-52732400	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr19:52697800-52732400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr19:52697800-52732600	Strong transcription	Primary T cells from cord blood	blood
26	chr19:52697800-52733000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:52698000-52730400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr19:52698000-52732200	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr19:52698000-52732200	Strong transcription	Dnd41	blood
30	chr19:52698200-52706400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr19:52698200-52714400	Weak transcription	Stomach Mucosa	stomach
32	chr19:52698200-52732000	Strong transcription	GM12878-XiMat	blood
33	chr19:52698200-52732400	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr19:52698200-52732400	Strong transcription	HepG2	liver
35	chr19:52698200-52732600	Strong transcription	Fetal Brain Female	brain
36	chr19:52698400-52732400	Strong transcription	Fetal Thymus	thymus
37	chr19:52698600-52732000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr19:52698800-52732400	Strong transcription	Liver	Liver
39	chr19:52700200-52712600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:52700400-52705000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr19:52700800-52732200	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr19:52701400-52705000	Genic enhancers	Brain Angular Gyrus	brain
43	chr19:52702200-52705000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr19:52702200-52731800	Strong transcription	Primary B cells from peripheral blood	blood
45	chr19:52702200-52732200	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr19:52702600-52732200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr19:52702800-52705000	Genic enhancers	Brain Anterior Caudate	brain
48	chr19:52702800-52707000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr19:52703000-52705000	Genic enhancers	Rectal Smooth Muscle	rectum
50	chr19:52703000-52731600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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