Variant report

Variant	rs12027850
Chromosome Location	chr1:220965909-220965910
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:220965572..220968372-chr1:220969216..220971838,2	MCF-7	breast:
2	chr1:220958940..220961119-chr1:220964763..220966587,2	MCF-7	breast:
3	chr1:220963256..220967868-chr1:220967973..220972005,4	MCF-7	breast:
4	chr1:220963259..220966041-chr1:220969331..220970964,2	K562	blood:
5	chr1:220958915..220961807-chr1:220964103..220968214,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186205	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10779415	0.83[CEU][hapmap]
rs10863562	0.83[CEU][hapmap]
rs11118597	0.83[CEU][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs11118599	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11118600	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12402066	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12562235	0.84[EUR][1000 genomes]
rs12568838	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17008609	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2642424	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs337147	0.83[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs337148	0.88[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs337150	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs365398	0.83[ASN][1000 genomes]
rs3795536	0.88[CEU][hapmap]
rs381023	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs421736	0.83[ASN][1000 genomes]
rs425473	0.83[CEU][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs4846662	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6657944	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6697965	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7518916	0.85[EUR][1000 genomes]
rs7519399	0.85[EUR][1000 genomes]
rs7519414	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7536276	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7539769	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7542648	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7542723	0.85[EUR][1000 genomes]
rs7553948	0.83[EUR][1000 genomes]
rs7556458	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7556561	0.84[EUR][1000 genomes]
rs9430990	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796146	chr1:220965474-220966649	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv1802688	chr1:220965474-220966649	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12027850	C1orf115	cis	Nerve Tibial	GTEx
rs12027850	C1orf115	Cis_1M	lymphoblastoid	RTeQTL
rs12027850	MOSC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220961000-220970200	Weak transcription	Fetal Kidney	kidney
2	chr1:220961000-220971200	Weak transcription	Spleen	Spleen
3	chr1:220961000-220973400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:220961000-220976800	Weak transcription	Ovary	ovary
5	chr1:220961000-220978200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:220961000-220982200	Weak transcription	Brain Substantia Nigra	brain
7	chr1:220961200-220971200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:220961400-220970600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:220961400-220983800	Weak transcription	Esophagus	oesophagus
10	chr1:220961600-220966600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:220961600-220969400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:220961600-220970000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:220961600-220970600	Weak transcription	Fetal Brain Female	brain
14	chr1:220961600-220971000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:220961600-220975000	Weak transcription	Brain Angular Gyrus	brain
16	chr1:220961600-220975200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:220961600-220983600	Weak transcription	Pancreas	Pancrea
18	chr1:220961800-220966000	Enhancers	Liver	Liver
19	chr1:220961800-220967000	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:220961800-220969600	Weak transcription	Stomach Mucosa	stomach
21	chr1:220961800-220969800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:220961800-220970000	Weak transcription	Fetal Stomach	stomach
23	chr1:220961800-220971600	Weak transcription	Brain Germinal Matrix	brain
24	chr1:220961800-220972000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:220961800-220974200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:220961800-220979800	Weak transcription	Right Atrium	heart
27	chr1:220961800-220981400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:220961800-220981600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:220961800-220983800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:220962000-220975000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:220962600-220966400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:220962600-220969800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:220964000-220974000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:220964400-220966000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:220964600-220966800	Weak transcription	Fetal Intestine Large	intestine
36	chr1:220964800-220970600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:220964800-220972000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr1:220964800-220978400	Weak transcription	Primary B cells from cord blood	blood
39	chr1:220965000-220968400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:220965000-220970000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:220965000-220972600	Weak transcription	Colonic Mucosa	Colon
42	chr1:220965000-220972600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr1:220965000-220980000	Weak transcription	Fetal Muscle Leg	muscle
44	chr1:220965200-220968200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
45	chr1:220965200-220969600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:220965200-220970000	Weak transcription	Lung	lung
47	chr1:220965200-220971000	Weak transcription	Colon Smooth Muscle	Colon
48	chr1:220965200-220971600	Weak transcription	Right Ventricle	heart
49	chr1:220965200-220979600	Weak transcription	Gastric	stomach
50	chr1:220965200-220985400	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links