Variant report

Variant	rs30197
Chromosome Location	chr5:75378560-75378561
allele	C/G
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	MXI1	chr5:75377350-75381483	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr5:75378454-75381515	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
SV2C	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs13162056	0.93[EUR][1000 genomes]
rs13174796	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1393205	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1423103	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1423104	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1553310	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs183766	0.83[ASN][1000 genomes]
rs1910051	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2254153	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2547455	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2547456	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs258612	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs258613	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs258614	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2731732	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2731733	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2731735	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28620	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28621	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs30191	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs30192	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30196	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30198	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30199	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs30202	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30204	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs30205	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs30206	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs30249	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7378518	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7443455	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7443586	0.81[AMR][1000 genomes]
rs993914	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[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	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv869885	chr5:75365786-75419656	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1033350	chr5:75367809-75538460	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs30197	CTC-235G5.3	cis	Nerve Tibial	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75377400-75381400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
2	chr5:75377600-75378600	Enhancers	Spleen	Spleen
3	chr5:75377600-75380000	Bivalent Enhancer	Fetal Brain Male	brain
4	chr5:75377600-75381000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr5:75377600-75381000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr5:75377600-75381200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr5:75377600-75381400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr5:75377600-75381600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr5:75377800-75378600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:75377800-75378600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
11	chr5:75377800-75378600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
12	chr5:75377800-75378600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:75377800-75378600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
14	chr5:75377800-75378600	Bivalent/Poised TSS	Colonic Mucosa	Colon
15	chr5:75377800-75378600	Enhancers	Ovary	ovary
16	chr5:75377800-75378800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:75377800-75378800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
18	chr5:75377800-75378800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
19	chr5:75377800-75379000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr5:75377800-75379000	Enhancers	Pancreas	Pancrea
21	chr5:75377800-75379200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
22	chr5:75377800-75379600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
23	chr5:75377800-75379600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
24	chr5:75377800-75379800	Bivalent Enhancer	Stomach Mucosa	stomach
25	chr5:75377800-75380000	Enhancers	Gastric	stomach
26	chr5:75377800-75380400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:75377800-75380400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr5:75377800-75381000	Bivalent Enhancer	Liver	Liver
29	chr5:75377800-75381200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
30	chr5:75377800-75381200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:75377800-75381200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr5:75378000-75378600	Bivalent Enhancer	Adipose Nuclei	Adipose
33	chr5:75378000-75378600	Active TSS	Brain Angular Gyrus	brain
34	chr5:75378000-75378600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:75378000-75378600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
36	chr5:75378000-75378800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
37	chr5:75378000-75379000	Bivalent Enhancer	Lung	lung
38	chr5:75378000-75379000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
39	chr5:75378000-75379200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:75378000-75379200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
41	chr5:75378000-75379800	Bivalent Enhancer	Esophagus	oesophagus
42	chr5:75378000-75380400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
43	chr5:75378000-75380400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
44	chr5:75378000-75380400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:75378000-75381200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
46	chr5:75378200-75378600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
47	chr5:75378200-75378600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:75378200-75378600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
49	chr5:75378200-75378600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr5:75378200-75378600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum

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