Variant report

Variant	rs12981654
Chromosome Location	chr19:36524282-36524283
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	chr19:36523422-36524305	U87	brain:	n/a	n/a
2	REST	chr19:36522810-36524431	H1-neurons	neurons:	n/a	chr19:36523635-36523642 chr19:36523011-36523029 chr19:36523488-36523501 chr19:36523770-36523783
3	POLR2A	chr19:36523709-36524350	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAZ	chr19:36522691-36524331	IMR90	lung:	n/a	chr19:36523773-36523783 chr19:36524013-36524022
5	POLR2A	chr19:36523555-36524302	U87	brain:	n/a	n/a
6	POLR2A	chr19:36523555-36524284	U87	brain:	n/a	n/a
7	POLR2A	chr19:36523428-36524285	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36512890..36520143-chr19:36521963..36527491,9	K562	blood:

Variant related genes	Relation type
CLIP3	TF binding region
ENSG00000105270	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10407011	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10414679	0.80[ASN][1000 genomes]
rs10414877	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10418015	0.91[JPT][hapmap]
rs10420353	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10421966	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10423651	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10425692	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10426582	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs12462432	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12462632	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12462674	0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12972490	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12976505	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12976812	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12977814	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12978482	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12979093	0.98[ASN][1000 genomes]
rs17639286	0.96[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2023865	0.84[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2239510	0.91[CEU][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34906485	0.90[ASN][1000 genomes]
rs35125548	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35875194	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3826995	0.92[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4461192	0.92[ASW][hapmap];0.85[CHB][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4805154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4805155	0.98[ASN][1000 genomes]
rs4806252	0.97[ASN][1000 genomes]
rs4806253	0.99[ASN][1000 genomes]
rs71337524	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs721542	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7245762	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs7247057	0.91[JPT][hapmap]
rs7250448	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7257383	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs7259592	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7260609	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8103569	0.92[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][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	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv911641	chr19:36473677-36536938	Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12981654	ZNF229	cis	parietal	SCAN
rs12981654	PSG9	cis	cerebellum	SCAN
rs12981654	CCDC97	cis	parietal	SCAN
rs12981654	GRIK5	cis	cerebellum	SCAN
rs12981654	CYP2B7P1	cis	parietal	SCAN
rs12981654	ZNF345	cis	parietal	SCAN
rs12981654	ATXN7L1	trans	parietal	SCAN
rs12981654	SHKBP1	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36506400-36544400	Weak transcription	GM12878-XiMat	blood
2	chr19:36506800-36532400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:36507000-36532200	Weak transcription	Hela-S3	cervix
4	chr19:36508800-36532400	Weak transcription	NHEK	skin
5	chr19:36513600-36525600	Weak transcription	K562	blood
6	chr19:36515200-36527600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr19:36515400-36544600	Weak transcription	Pancreas	Pancrea
8	chr19:36516400-36532400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr19:36517000-36526400	Weak transcription	HepG2	liver
10	chr19:36518800-36532200	Weak transcription	A549	lung
11	chr19:36522200-36524400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:36522200-36524400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:36522800-36524400	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr19:36522800-36524400	Active TSS	Rectal Smooth Muscle	rectum
15	chr19:36523000-36524400	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr19:36523000-36524400	Active TSS	Colon Smooth Muscle	Colon
17	chr19:36523000-36524400	Weak transcription	Dnd41	blood
18	chr19:36523000-36524600	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr19:36523200-36524400	Enhancers	Primary B cells from peripheral blood	blood
20	chr19:36523200-36524400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:36523200-36524400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:36523200-36524400	Active TSS	Brain Hippocampus Middle	brain
23	chr19:36523200-36524400	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr19:36523800-36524400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr19:36523800-36524400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr19:36523800-36524400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:36523800-36524400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:36523800-36524400	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr19:36523800-36525800	Weak transcription	Gastric	stomach
30	chr19:36524000-36524400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:36524000-36524400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:36524000-36524400	Enhancers	Primary T cells fromperipheralblood	blood
33	chr19:36524000-36524400	Flanking Active TSS	Brain Angular Gyrus	brain
34	chr19:36524000-36524400	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr19:36524000-36524400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr19:36524000-36524400	Flanking Active TSS	Brain Substantia Nigra	brain
37	chr19:36524000-36524400	Flanking Active TSS	Fetal Brain Male	brain
38	chr19:36524000-36524400	Flanking Active TSS	Fetal Brain Female	brain
39	chr19:36524000-36524400	Flanking Active TSS	Fetal Kidney	kidney
40	chr19:36524000-36524400	Flanking Active TSS	Fetal Lung	lung
41	chr19:36524000-36524400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
42	chr19:36524000-36524400	Flanking Active TSS	Osteobl	bone
43	chr19:36524000-36525400	Weak transcription	Lung	lung
44	chr19:36524000-36525600	Weak transcription	Liver	Liver
45	chr19:36524000-36525600	Weak transcription	Spleen	Spleen
46	chr19:36524000-36526000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr19:36524000-36526000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:36524000-36526000	Weak transcription	Esophagus	oesophagus
49	chr19:36524000-36529400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr19:36524000-36532000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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