Variant report

Variant	rs10877020
Chromosome Location	chr12:58188014-58188015
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58177143..58179601-chr12:58187871..58190318,2	K562	blood:
2	chr12:58146517..58149698-chr12:58186091..58190303,5	MCF-7	breast:
3	chr12:58165686..58169412-chr12:58185900..58189791,5	MCF-7	breast:
4	chr12:58183737..58188144-chr12:58191635..58196176,5	MCF-7	breast:
5	chr12:58175367..58177051-chr12:58187510..58189205,2	K562	blood:
6	chr12:58153606..58155197-chr12:58186466..58188523,2	K562	blood:
7	chr12:58175367..58177033-chr12:58187510..58189407,2	K562	blood:
8	chr12:58175481..58178584-chr12:58184682..58189368,5	MCF-7	breast:
9	chr12:58179133..58181417-chr12:58186670..58188914,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000123297	Chromatin interaction
ENSG00000266465	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000135407	Chromatin interaction
ENSG00000139266	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11172337	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12368653	0.89[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.81[EUR][1000 genomes]
rs12371356	0.89[CEU][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap]
rs2270777	0.82[GIH][hapmap]
rs2277326	0.87[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2307097	0.87[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3816896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760340	0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10877020	RDH5	cis	parietal	SCAN
rs10877020	TSFM	cis	lymphoblastoid	seeQTL
rs10877020	XRCC6BP1	cis	Artery Tibial	GTEx
rs10877020	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs10877020	NR3C1	trans	lymphoblastoid	RTeQTL
rs10877020	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs10877020	FAM119B	cis	lymphoblastoid	seeQTL
rs10877020	FAM119B	cis	cerebellum	SCAN
rs10877020	KRT75	cis	cerebellum	SCAN
rs10877020	XRCC6BP1	cis	Whole Blood	GTEx
rs10877020	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10877020	FAM119B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58177200-58189800	Weak transcription	Small Intestine	intestine
2	chr12:58177200-58197200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:58177400-58190000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:58177400-58192800	Weak transcription	Stomach Mucosa	stomach
5	chr12:58177400-58200400	Weak transcription	Fetal Heart	heart
6	chr12:58177400-58216400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:58177800-58188400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:58177800-58189600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:58177800-58191200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:58177800-58192200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:58177800-58198400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr12:58177800-58198400	Strong transcription	Fetal Muscle Leg	muscle
13	chr12:58177800-58199000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:58178000-58188600	Strong transcription	Fetal Lung	lung
15	chr12:58178000-58193200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:58178000-58194200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr12:58178000-58197200	Strong transcription	Primary B cells from peripheral blood	blood
18	chr12:58178000-58197600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr12:58178000-58198200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:58178000-58198200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:58178000-58198200	Strong transcription	Fetal Thymus	thymus
22	chr12:58178200-58197000	Strong transcription	Fetal Intestine Large	intestine
23	chr12:58178200-58197200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:58178200-58198200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr12:58178400-58191000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:58178400-58194000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:58178600-58191400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:58178600-58207600	Strong transcription	Liver	Liver
29	chr12:58179000-58188600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr12:58179000-58191400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr12:58179000-58191400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr12:58179000-58192000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:58179000-58192200	Strong transcription	Adipose Nuclei	Adipose
34	chr12:58179000-58193200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:58179000-58196800	Strong transcription	Thymus	Thymus
36	chr12:58179000-58197600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr12:58179000-58198200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:58179200-58199000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:58179400-58197400	Strong transcription	Duodenum Mucosa	Duodenum
40	chr12:58179600-58193800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:58179800-58194000	Strong transcription	Dnd41	blood
42	chr12:58180600-58189000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:58180600-58190000	Weak transcription	Gastric	stomach
44	chr12:58180600-58191400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:58181000-58189600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr12:58181000-58189600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr12:58181200-58189400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:58181200-58190600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr12:58181400-58216000	Weak transcription	Fetal Brain Male	brain
50	chr12:58182000-58189000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links