Variant report

Variant	rs30198
Chromosome Location	chr5:75378769-75378770
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	SUZ12	chr5:75378740-75380029	H1-hESC	embryonic stem cell:	n/a	n/a
2	HA-E2F1	chr5:75378726-75379766	MCF-7	breast:	n/a	chr5:75378949-75378958 chr5:75379166-75379173 chr5:75379514-75379521 chr5:75378946-75378958 chr5:75379269-75379279 chr5:75379165-75379177 chr5:75379166-75379173 chr5:75379723-75379732 chr5:75379166-75379173
3	SIN3A	chr5:75378597-75380256	H1-hESC	embryonic stem cell:	n/a	chr5:75379100-75379109 chr5:75378803-75378816 chr5:75379099-75379113 chr5:75379413-75379422
4	HDAC2	chr5:75378713-75379504	MCF-7	breast:	n/a	n/a
5	ZNF263	chr5:75378631-75380262	HEK293-T-REx	kidney:	n/a	chr5:75379130-75379139 chr5:75379109-75379118 chr5:75379161-75379182
6	GATA2	chr5:75378706-75381050	SH-SY5Y	brain:	n/a	chr5:75379607-75379624 chr5:75380885-75380892
7	MXI1	chr5:75377350-75381483	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr5:75378769-75378858	MCF-7	breast:	n/a	n/a
9	ZNF143	chr5:75378675-75379476	H1-hESC	embryonic stem cell:	n/a	chr5:75379269-75379279 chr5:75379413-75379423 chr5:75379084-75379094 chr5:75379408-75379426
10	POLR2A	chr5:75378454-75381515	H1-neurons	neurons:	n/a	n/a
11	CTBP2	chr5:75378607-75380344	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr5:75378720-75378870	GM12871	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75378752..75382586-chr5:75384314..75388337,4	K562	blood:

Variant related genes	Relation type
SV2C	TF binding region
ENSG00000252833	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs13162056	0.82[EUR][1000 genomes]
rs13174796	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1393205	0.82[EUR][1000 genomes]
rs1423103	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1423104	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1501905	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs1553310	0.81[EUR][1000 genomes]
rs183766	0.89[CHD][hapmap]
rs183767	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs187285	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs1910051	0.81[EUR][1000 genomes]
rs2254153	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2547455	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2547456	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs258612	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs258613	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs258614	0.88[CEU][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs258621	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2731732	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2731735	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28620	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28621	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2937705	0.84[CEU][hapmap]
rs30191	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30192	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30196	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30197	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30199	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30202	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs30204	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs30205	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs30206	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs30249	0.81[CHB][hapmap];0.83[EUR][1000 genomes]
rs7378518	0.82[EUR][1000 genomes]
rs7443455	0.82[EUR][1000 genomes]
rs993914	0.83[EUR][1000 genomes];0.82[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

No data

Chromatin state (count:90 , 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	chr5:75377600-75380000	Bivalent Enhancer	Fetal Brain Male	brain
3	chr5:75377600-75381000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr5:75377600-75381000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr5:75377600-75381200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr5:75377600-75381400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr5:75377600-75381600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr5:75377800-75378800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:75377800-75378800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
10	chr5:75377800-75378800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
11	chr5:75377800-75379000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr5:75377800-75379000	Enhancers	Pancreas	Pancrea
13	chr5:75377800-75379200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
14	chr5:75377800-75379600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
15	chr5:75377800-75379600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:75377800-75379800	Bivalent Enhancer	Stomach Mucosa	stomach
17	chr5:75377800-75380000	Enhancers	Gastric	stomach
18	chr5:75377800-75380400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:75377800-75380400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:75377800-75381000	Bivalent Enhancer	Liver	Liver
21	chr5:75377800-75381200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
22	chr5:75377800-75381200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:75377800-75381200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr5:75378000-75378800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
25	chr5:75378000-75379000	Bivalent Enhancer	Lung	lung
26	chr5:75378000-75379000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
27	chr5:75378000-75379200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:75378000-75379200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
29	chr5:75378000-75379800	Bivalent Enhancer	Esophagus	oesophagus
30	chr5:75378000-75380400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
31	chr5:75378000-75380400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
32	chr5:75378000-75380400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:75378000-75381200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:75378200-75378800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:75378200-75378800	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr5:75378200-75378800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:75378200-75378800	Weak transcription	Right Atrium	heart
38	chr5:75378200-75378800	Bivalent/Poised TSS	NHEK	skin
39	chr5:75378200-75379000	Bivalent Enhancer	Fetal Stomach	stomach
40	chr5:75378200-75379200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
41	chr5:75378400-75378800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
42	chr5:75378400-75378800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
43	chr5:75378400-75378800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr5:75378400-75379000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:75378400-75379000	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
46	chr5:75378400-75379000	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
47	chr5:75378400-75379000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
48	chr5:75378400-75379600	Active TSS	Brain Substantia Nigra	brain
49	chr5:75378400-75379600	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
50	chr5:75378400-75379800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood

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