Variant report

Variant	rs73175079
Chromosome Location	chr13:37624119-37624120
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr13:37624060-37624210	HA-sp	spinal cord:	n/a	n/a
2	CTCF	chr13:37624020-37624170	HPF	lung:	n/a	n/a
3	CTCF	chr13:37624080-37624230	SK-N-SH_RA	brain:	n/a	n/a
4	CTCF	chr13:37624100-37624250	HEK293	kidney:	n/a	n/a
5	CTCF	chr13:37624000-37624150	RPTEC	kidney:	n/a	n/a
6	CTCF	chr13:37624102-37624210	MCF-7	breast:	n/a	n/a
7	CTCF	chr13:37624080-37624230	HPAF	blood vessel:	n/a	n/a
8	RAD21	chr13:37623991-37624236	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr13:37624060-37624210	HPF	lung:	n/a	n/a
10	CTCF	chr13:37624020-37624170	HAc	cerebellar:	n/a	n/a
11	CTCF	chr13:37624076-37624215	HUVEC	blood vessel:	n/a	n/a
12	CTCF	chr13:37624040-37624190	GM12871	blood:	n/a	n/a
13	CTCF	chr13:37624113-37624161	MCF-7	breast:	n/a	n/a
14	CTCF	chr13:37624080-37624230	HCPEpiC	choroid plexus:	n/a	n/a
15	CTCF	chr13:37624020-37624170	HRPEpiC	eye:	n/a	n/a
16	CTCF	chr13:37624020-37624170	HCT-116	colon:	n/a	n/a
17	CTCF	chr13:37624040-37624190	HFF-Myc	foreskin:	n/a	n/a
18	CTCF	chr13:37624060-37624210	HCFaa	heart:	n/a	n/a
19	CTCF	chr13:37624020-37624170	MCF-7	breast:	n/a	n/a
20	CTCF	chr13:37624060-37624210	HPAF	blood vessel:	n/a	n/a
21	CTCF	chr13:37624060-37624210	HMF	breast:	n/a	n/a
22	CTCF	chr13:37624020-37624170	HCM	heart:	n/a	n/a
23	CTCF	chr13:37624060-37624210	HUVEC	blood vessel:	n/a	n/a
24	CTCF	chr13:37624060-37624210	GM12873	blood:	n/a	n/a
25	CTCF	chr13:37624097-37624218	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr13:37624040-37624190	K562	blood:	n/a	n/a
27	CTCF	chr13:37623999-37624324	K562	blood:	n/a	n/a
28	CTCF	chr13:37624069-37624227	K562	blood:	n/a	n/a
29	CTCF	chr13:37624080-37624230	BE2_C	brain:	n/a	n/a
30	CTCF	chr13:37624080-37624230	HBMEC	blood vessel:	n/a	n/a
31	CTCF	chr13:37624060-37624210	GM12866	blood:	n/a	n/a
32	CTCF	chr13:37624080-37624230	HRE	kidney:	n/a	n/a
33	CTCF	chr13:37624024-37624224	GM12878	blood:	n/a	n/a
34	CTCF	chr13:37624111-37624179	GM13977	blood:	n/a	n/a
35	CTCF	chr13:37624060-37624210	HMEC	breast:	n/a	n/a
36	CTCF	chr13:37624040-37624190	HepG2	liver:	n/a	n/a
37	CTCF	chr13:37624020-37624170	AG04450	lung:	n/a	n/a
38	CTCF	chr13:37624100-37624250	HA-sp	spinal cord:	n/a	n/a
39	CTCF	chr13:37624100-37624250	HCPEpiC	choroid plexus:	n/a	n/a
40	CTCF	chr13:37624040-37624190	HBMEC	blood vessel:	n/a	n/a
41	CTCF	chr13:37624080-37624230	RPTEC	kidney:	n/a	n/a
42	CTCF	chr13:37624060-37624210	NB4	blood:	n/a	n/a
43	CTCF	chr13:37624020-37624170	AG10803	skin:	n/a	n/a
44	CTCF	chr13:37624080-37624230	K562	blood:	n/a	n/a
45	CTCF	chr13:37624017-37624244	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr13:37624040-37624190	BJ	skin:	n/a	n/a
47	CTCF	chr13:37624040-37624190	AG09319	gingival:	n/a	n/a
48	CTCF	chr13:37624100-37624250	HMEC	breast:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:37573365..37576545-chr13:37622810..37625636,4	MCF-7	breast:
2	chr13:37623154..37627284-chr13:37630471..37633979,5	MCF-7	breast:

No data

Variant related genes	Relation type
SUPT20H	TF binding region
ENSG00000120699	Chromatin interaction
ENSG00000120697	Chromatin interaction
ENSG00000102710	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1199951	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1199956	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1199960	0.80[EUR][1000 genomes]
rs1199962	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1199963	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1199966	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1199972	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1199974	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1199977	0.80[EUR][1000 genomes]
rs1199978	0.80[EUR][1000 genomes]
rs1199979	0.87[EUR][1000 genomes]
rs1199980	0.80[EUR][1000 genomes]
rs1199981	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1199982	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1199983	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1199984	0.87[EUR][1000 genomes]
rs1199986	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1199987	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1199988	0.88[EUR][1000 genomes]
rs1199989	0.88[EUR][1000 genomes]
rs1336755	0.88[EUR][1000 genomes]
rs1543738	0.94[EUR][1000 genomes]
rs1764481	0.80[EUR][1000 genomes]
rs1764483	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1764484	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1764486	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1764487	0.88[EUR][1000 genomes]
rs1764488	0.82[EUR][1000 genomes]
rs1924418	0.93[EUR][1000 genomes]
rs1924426	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1937760	0.82[EUR][1000 genomes]
rs2093817	0.93[EUR][1000 genomes]
rs2211618	0.88[EUR][1000 genomes]
rs2323392	0.85[EUR][1000 genomes]
rs2669893	0.88[EUR][1000 genomes]
rs2785620	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2801799	0.91[AFR][1000 genomes]
rs2997189	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2997190	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2997193	0.82[EUR][1000 genomes]
rs3858859	0.88[EUR][1000 genomes]
rs4291799	0.91[AFR][1000 genomes]
rs6563508	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6563509	0.93[EUR][1000 genomes]
rs7320899	0.93[EUR][1000 genomes]
rs7326688	0.88[EUR][1000 genomes]
rs7334233	1.00[AFR][1000 genomes]
rs7339296	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7989380	0.88[EUR][1000 genomes]
rs7995098	0.80[EUR][1000 genomes]
rs7997310	0.93[EUR][1000 genomes]
rs8001662	0.93[EUR][1000 genomes]
rs9532005	1.00[AFR][1000 genomes]
rs9547721	0.91[EUR][1000 genomes]
rs9547725	0.87[EUR][1000 genomes]
rs9576154	1.00[AFR][1000 genomes]
rs9576162	0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73175079	SUPT20H	cis	Whole Blood	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37575400-37631200	Weak transcription	Stomach Mucosa	stomach
2	chr13:37576600-37625800	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr13:37577000-37624400	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr13:37577200-37625200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr13:37577200-37625800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr13:37577200-37625800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr13:37589200-37625800	Strong transcription	Fetal Thymus	thymus
8	chr13:37601800-37625200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr13:37606800-37632400	Weak transcription	Hela-S3	cervix
10	chr13:37607800-37631000	Weak transcription	Pancreas	Pancrea
11	chr13:37608800-37631800	Weak transcription	Psoas Muscle	Psoas
12	chr13:37610000-37631000	Weak transcription	Lung	lung
13	chr13:37610000-37632200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr13:37610200-37626000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:37610600-37632000	Weak transcription	Small Intestine	intestine
16	chr13:37610800-37625800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr13:37611400-37631000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr13:37613600-37632400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr13:37613600-37632600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr13:37616400-37632200	Weak transcription	A549	lung
21	chr13:37616800-37631000	Weak transcription	Right Ventricle	heart
22	chr13:37616800-37632200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr13:37616800-37632200	Weak transcription	NHLF	lung
24	chr13:37617000-37627000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr13:37617000-37632400	Weak transcription	K562	blood
26	chr13:37617400-37631000	Weak transcription	NHEK	skin
27	chr13:37617600-37632600	Weak transcription	Brain Substantia Nigra	brain
28	chr13:37617600-37632800	Weak transcription	Brain Hippocampus Middle	brain
29	chr13:37617600-37632800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr13:37617600-37632800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr13:37617800-37631800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr13:37618000-37627400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr13:37618000-37631800	Weak transcription	Gastric	stomach
34	chr13:37618000-37632200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr13:37618000-37632400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr13:37618000-37632400	Weak transcription	Brain Angular Gyrus	brain
37	chr13:37618000-37632400	Weak transcription	Fetal Kidney	kidney
38	chr13:37618000-37632600	Weak transcription	Thymus	Thymus
39	chr13:37618000-37632800	Weak transcription	Ovary	ovary
40	chr13:37618000-37633000	Weak transcription	Spleen	Spleen
41	chr13:37618200-37630600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr13:37618200-37630800	Weak transcription	Fetal Stomach	stomach
43	chr13:37618200-37630800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr13:37618200-37631000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr13:37618200-37631000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr13:37618200-37632200	Weak transcription	Brain Germinal Matrix	brain
47	chr13:37618200-37632400	Weak transcription	Fetal Brain Male	brain
48	chr13:37618200-37632600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr13:37618200-37633000	Weak transcription	Esophagus	oesophagus
50	chr13:37618800-37632200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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