Variant report

Variant	rs172786
Chromosome Location	chr19:37712984-37712985
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	chr19:37712955-37713142	K562	blood:	n/a	n/a
2	GATA2	chr19:37712746-37713050	SH-SY5Y	brain:	n/a	n/a
3	GATA3	chr19:37712881-37713194	SH-SY5Y	brain:	n/a	n/a
4	NFYA	chr19:37712903-37713072	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37707730..37710581-chr19:37712295..37715245,3	MCF-7	breast:
2	chr19:37700579..37702505-chr19:37711675..37713622,2	K562	blood:

Variant related genes	Relation type
ZNF585B	TF binding region
ZNF383	TF binding region
ENSG00000267360	Chromatin interaction
ENSG00000245680	Chromatin interaction
ENSG00000188283	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10402144	0.93[EUR][1000 genomes]
rs10411236	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234257	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1234259	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234260	0.89[ASN][1000 genomes]
rs12459637	0.85[JPT][hapmap]
rs1657506	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1664696	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs188877	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28613334	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs320877	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs320879	0.96[CEU][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs320889	0.97[EUR][1000 genomes]
rs320891	1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs860386	0.96[CEU][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers 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 target site	73 gene(s)	inside rSNPs	diseases
2	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv911654	chr19:37487632-37758082	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv911655	chr19:37646745-37758082	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv961287	chr19:37708789-37742224	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs172786	CEACAM20	cis	parietal	SCAN
rs172786	CBLC	cis	parietal	SCAN
rs172786	FBXO17	cis	cerebellum	SCAN
rs172786	C19orf33	cis	cerebellum	SCAN
rs172786	AXL	cis	cerebellum	SCAN
rs172786	LIPE	cis	cerebellum	SCAN
rs172786	MEGF8	cis	cerebellum	SCAN
rs172786	CATSPERG	cis	parietal	SCAN
rs172786	SNRPD2	cis	parietal	SCAN
rs172786	SSBP2	cis	Temporal Cortex	GTEx
rs172786	SUPT5H	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37709600-37714800	ZNF genes & repeats	A549	lung
2	chr19:37709800-37718400	Weak transcription	Aorta	Aorta
3	chr19:37710000-37716000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:37710000-37716000	Weak transcription	Fetal Thymus	thymus
5	chr19:37710000-37717000	Weak transcription	NH-A	brain
6	chr19:37710000-37717200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:37710000-37718400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:37710000-37720800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr19:37710000-37721000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:37710000-37728600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:37710200-37713000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr19:37710200-37713400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:37710200-37713600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr19:37710200-37713600	Strong transcription	Fetal Stomach	stomach
15	chr19:37710200-37713800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
16	chr19:37710200-37714000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:37710200-37714000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:37710200-37714000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr19:37710200-37715200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr19:37710200-37715400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr19:37710200-37715400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr19:37710200-37715800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr19:37710200-37715800	Weak transcription	Brain Anterior Caudate	brain
24	chr19:37710200-37716000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr19:37710200-37716200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr19:37710200-37716200	Weak transcription	Brain Germinal Matrix	brain
27	chr19:37710200-37716200	Weak transcription	Brain Hippocampus Middle	brain
28	chr19:37710200-37716200	Weak transcription	Colonic Mucosa	Colon
29	chr19:37710200-37716200	Weak transcription	Fetal Kidney	kidney
30	chr19:37710200-37716200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr19:37710200-37716200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr19:37710200-37716200	Weak transcription	HSMMtube	muscle
33	chr19:37710200-37716400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:37710200-37716400	Weak transcription	Colon Smooth Muscle	Colon
35	chr19:37710200-37716800	Weak transcription	Small Intestine	intestine
36	chr19:37710200-37717000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr19:37710200-37718400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr19:37710200-37718800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:37710200-37718800	Weak transcription	HUVEC	blood vessel
40	chr19:37710200-37718800	Weak transcription	NHLF	lung
41	chr19:37710200-37719000	Weak transcription	HepG2	liver
42	chr19:37710200-37720800	Weak transcription	K562	blood
43	chr19:37710200-37723800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
44	chr19:37710200-37725600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr19:37710200-37725600	Weak transcription	Fetal Heart	heart
46	chr19:37710200-37728600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:37710400-37713400	Weak transcription	Ovary	ovary
48	chr19:37710400-37713600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr19:37710400-37713600	Strong transcription	Fetal Muscle Leg	muscle
50	chr19:37710400-37713600	Weak transcription	HSMM	muscle

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