Variant report

Variant	rs12577614
Chromosome Location	chr11:74671100-74671101
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74670533..74672513-chr11:74690416..74693115,2	MCF-7	breast:
2	chr11:74665537..74669916-chr11:74669929..74673689,6	K562	blood:
3	chr11:74669969..74672134-chr11:74806047..74808621,2	K562	blood:
4	chr11:74665174..74667770-chr11:74669572..74672146,3	MCF-7	breast:
5	chr11:74660556..74662199-chr11:74670224..74671881,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118363	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10160410	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10751241	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10793105	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10793107	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10793108	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899045	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899051	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10899052	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10899053	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10899054	0.87[AMR][1000 genomes]
rs10899058	0.83[AMR][1000 genomes]
rs10899059	0.82[AMR][1000 genomes]
rs10899060	0.80[AMR][1000 genomes]
rs11236244	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11236281	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11236282	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11236289	0.85[AMR][1000 genomes]
rs11236290	0.87[AMR][1000 genomes]
rs11236294	0.85[AMR][1000 genomes]
rs11236296	0.80[AMR][1000 genomes]
rs11603294	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12221841	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12225372	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12225387	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12419113	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12419929	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12421899	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12574850	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12575200	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12576129	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12577127	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1371410	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17133461	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2119028	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2165162	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2165163	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298746	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2304683	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3814726	0.85[ASN][1000 genomes]
rs4245440	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4387374	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4483614	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4944061	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4944950	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4944960	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4944961	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4944963	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4944965	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4944968	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56194145	0.88[AMR][1000 genomes]
rs59143825	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59328242	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61671395	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61734374	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61894779	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61894839	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7102619	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7105085	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7128739	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs725460	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7396866	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7483351	0.85[AMR][1000 genomes]
rs7928381	0.85[ASN][1000 genomes]
rs919877	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9787775	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9787897	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][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	nsv832210	chr11:74562782-74732133	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs12577614	XRRA1	cis	Esophagus Mucosa	GTEx
rs12577614	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs12577614	XRRA1	cis	Adipose Subcutaneous	GTEx
rs12577614	XRRA1	cis	Esophagus Muscularis	GTEx
rs12577614	XRRA1	cis	lung	GTEx
rs12577614	XRRA1	cis	Muscle Skeletal	GTEx
rs12577614	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs12577614	XRRA1	cis	Stomach	GTEx
rs12577614	XRRA1	cis	Thyroid	GTEx
rs12577614	XRRA1	cis	Artery Tibial	GTEx
rs12577614	XRRA1	cis	Nerve Tibial	GTEx
rs12577614	XRRA1	cis	Artery Aorta	GTEx
rs12577614	RP11-147I3.1	cis	Thyroid	GTEx
rs12577614	XRRA1	cis	Heart Left Ventricle	GTEx
rs12577614	XRRA1	cis	Whole Blood	GTEx
rs12577614	RP11-147I3.1	cis	Muscle Skeletal	GTEx
rs12577614	RP11-147I3.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74661200-74688600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:74661600-74686000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:74661800-74672600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr11:74661800-74675000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr11:74661800-74699200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr11:74661800-74699400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:74662000-74677600	Weak transcription	HSMMtube	muscle
8	chr11:74662000-74680800	Weak transcription	Fetal Kidney	kidney
9	chr11:74662000-74682200	Weak transcription	Aorta	Aorta
10	chr11:74662000-74682800	Weak transcription	Colonic Mucosa	Colon
11	chr11:74662200-74671600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:74662200-74672800	Weak transcription	Gastric	stomach
13	chr11:74662200-74672800	Weak transcription	Stomach Mucosa	stomach
14	chr11:74662200-74677000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr11:74662200-74677200	Weak transcription	Fetal Muscle Leg	muscle
16	chr11:74662200-74677200	Weak transcription	Thymus	Thymus
17	chr11:74662200-74677800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr11:74662200-74677800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr11:74662200-74699600	Weak transcription	Esophagus	oesophagus
20	chr11:74662400-74673000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr11:74662400-74675200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr11:74662400-74677800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr11:74662400-74677800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:74662400-74677800	Weak transcription	Fetal Stomach	stomach
25	chr11:74662400-74680600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr11:74662400-74691400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr11:74662600-74676600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr11:74662600-74682800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:74662600-74686000	Weak transcription	Fetal Brain Male	brain
30	chr11:74662800-74677800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr11:74662800-74682200	Weak transcription	Lung	lung
32	chr11:74663200-74680000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr11:74663600-74671800	Weak transcription	Fetal Brain Female	brain
34	chr11:74664000-74680400	Weak transcription	HMEC	breast
35	chr11:74664200-74671600	Weak transcription	NH-A	brain
36	chr11:74664200-74677200	Weak transcription	Fetal Lung	lung
37	chr11:74664400-74675800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr11:74664400-74678000	Weak transcription	Brain Germinal Matrix	brain
39	chr11:74664600-74675800	Weak transcription	Fetal Intestine Large	intestine
40	chr11:74664600-74677800	Weak transcription	NHLF	lung
41	chr11:74665200-74672200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr11:74665600-74686000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:74665800-74675800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:74666200-74674800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr11:74666200-74677200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr11:74666400-74671800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr11:74666600-74674200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr11:74666600-74675800	Weak transcription	A549	lung
49	chr11:74667400-74672000	Genic enhancers	K562	blood
50	chr11:74667600-74689000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links