Variant report

Variant	rs2785620
Chromosome Location	chr13:37623269-37623270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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:

Variant related genes	Relation type
ENSG00000102710	Chromatin interaction
ENSG00000120699	Chromatin interaction
ENSG00000120697	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1199951	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1199956	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1199960	0.84[EUR][1000 genomes]
rs1199962	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1199963	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1199966	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1199972	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1199974	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1199977	0.84[EUR][1000 genomes]
rs1199978	0.84[EUR][1000 genomes]
rs1199979	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1199980	0.84[EUR][1000 genomes]
rs1199981	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199982	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199983	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1199984	1.00[CEU][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1199986	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1199987	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1199988	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1199989	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12429860	0.80[EUR][1000 genomes]
rs1336755	0.92[EUR][1000 genomes]
rs1543738	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1764481	0.84[EUR][1000 genomes]
rs1764483	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1764484	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1764486	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1764487	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1764488	0.85[EUR][1000 genomes]
rs1924418	0.97[EUR][1000 genomes]
rs1924422	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs1924426	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1937760	0.85[EUR][1000 genomes]
rs1937761	0.90[CEU][hapmap]
rs2093817	1.00[CEU][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs2147169	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2181788	0.81[CEU][hapmap]
rs2211618	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2323165	0.90[CEU][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs2323392	0.89[EUR][1000 genomes]
rs2669893	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2769543	0.89[CEU][hapmap]
rs2801799	0.86[AMR][1000 genomes]
rs2997189	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2997190	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2997193	0.81[EUR][1000 genomes]
rs3858859	0.93[EUR][1000 genomes]
rs4291799	0.90[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs4941854	0.90[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes]
rs4941855	0.87[AMR][1000 genomes]
rs4941856	0.90[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs4943441	1.00[CEU][hapmap];0.93[TSI][hapmap]
rs6563506	0.81[CEU][hapmap]
rs6563507	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6563508	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6563509	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs675108	0.82[CEU][hapmap]
rs688280	0.83[GIH][hapmap]
rs73175079	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7317750	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs7320899	0.97[EUR][1000 genomes]
rs7321129	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs7326688	0.92[EUR][1000 genomes]
rs7334233	0.81[AMR][1000 genomes]
rs7338929	0.90[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs7339296	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7982674	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7983986	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs7989205	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs7989380	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7991057	0.90[CEU][hapmap];0.81[AMR][1000 genomes]
rs7995098	0.84[EUR][1000 genomes]
rs7997310	1.00[CEU][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs8001662	0.97[EUR][1000 genomes]
rs9315459	0.81[AMR][1000 genomes]
rs9532001	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs9532004	0.90[CEU][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap]
rs9532005	0.90[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes]
rs9547707	0.90[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap]
rs9547715	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs9547717	0.81[CEU][hapmap];1.00[GIH][hapmap]
rs9547718	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs9547721	0.95[EUR][1000 genomes]
rs9547725	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9576153	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9576154	0.90[CEU][hapmap];0.81[AMR][1000 genomes]
rs9576162	0.92[EUR][1000 genomes]
rs9603121	0.90[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2785620	SUPT20H	cis	Whole Blood	GTEx
rs2785620	FAM48A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 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	chr13:37576200-37623800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr13:37576400-37623800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr13:37576600-37625800	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr13:37577000-37623400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr13:37577000-37624400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr13:37577200-37625200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr13:37577200-37625800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr13:37577200-37625800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr13:37577600-37623600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr13:37583000-37623400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr13:37586800-37623400	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr13:37589200-37625800	Strong transcription	Fetal Thymus	thymus
14	chr13:37589600-37623800	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr13:37601800-37625200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr13:37604200-37623600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr13:37604800-37623600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr13:37606800-37632400	Weak transcription	Hela-S3	cervix
19	chr13:37607800-37631000	Weak transcription	Pancreas	Pancrea
20	chr13:37608400-37624000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr13:37608800-37631800	Weak transcription	Psoas Muscle	Psoas
22	chr13:37610000-37631000	Weak transcription	Lung	lung
23	chr13:37610000-37632200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr13:37610200-37626000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr13:37610600-37632000	Weak transcription	Small Intestine	intestine
26	chr13:37610800-37625800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr13:37611400-37623400	Strong transcription	GM12878-XiMat	blood
28	chr13:37611400-37631000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr13:37613600-37632400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr13:37613600-37632600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr13:37616400-37632200	Weak transcription	A549	lung
32	chr13:37616800-37631000	Weak transcription	Right Ventricle	heart
33	chr13:37616800-37632200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr13:37616800-37632200	Weak transcription	NHLF	lung
35	chr13:37617000-37627000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr13:37617000-37632400	Weak transcription	K562	blood
37	chr13:37617400-37631000	Weak transcription	NHEK	skin
38	chr13:37617600-37623600	Strong transcription	HUVEC	blood vessel
39	chr13:37617600-37632600	Weak transcription	Brain Substantia Nigra	brain
40	chr13:37617600-37632800	Weak transcription	Brain Hippocampus Middle	brain
41	chr13:37617600-37632800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr13:37617600-37632800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr13:37617800-37631800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr13:37618000-37627400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr13:37618000-37631800	Weak transcription	Gastric	stomach
46	chr13:37618000-37632200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr13:37618000-37632400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr13:37618000-37632400	Weak transcription	Brain Angular Gyrus	brain
49	chr13:37618000-37632400	Weak transcription	Fetal Kidney	kidney
50	chr13:37618000-37632600	Weak transcription	Thymus	Thymus

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