Variant report

Variant	rs2274738
Chromosome Location	chr1:86119898-86119899
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85950441..85953344-chr1:86117969..86119988,2	MCF-7	breast:
2	chr1:86114750..86117708-chr1:86118928..86121953,3	MCF-7	breast:
3	chr1:86048276..86051402-chr1:86117655..86121071,4	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10158408	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10493773	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10493774	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161649	0.89[CEU][hapmap]
rs12067749	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12075929	0.92[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes]
rs12564080	0.88[CEU][hapmap]
rs12722770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12739713	0.88[CEU][hapmap]
rs12751296	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12754358	0.96[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17394091	0.82[AFR][1000 genomes]
rs17398175	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs17398321	0.83[ASN][1000 genomes]
rs2069208	0.88[CEU][hapmap]
rs34746573	0.82[AFR][1000 genomes]
rs3767163	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs414618	0.81[CEU][hapmap]
rs55654440	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6576784	0.88[CEU][hapmap]
rs6667672	0.83[AMR][1000 genomes]
rs6697548	0.87[AMR][1000 genomes]
rs6698578	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7354850	0.84[ASN][1000 genomes]
rs7523292	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2274738	C1orf181	Cis_1M	lymphoblastoid	RTeQTL
rs2274738	ZNHIT6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86095400-86134800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:86103400-86173000	Weak transcription	Pancreas	Pancrea
3	chr1:86103600-86120200	Weak transcription	HMEC	breast
4	chr1:86103600-86141200	Weak transcription	Thymus	Thymus
5	chr1:86103600-86142200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:86103600-86145400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:86103600-86145600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:86103600-86157400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:86103600-86172600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:86103600-86172600	Weak transcription	Gastric	stomach
11	chr1:86106000-86141200	Weak transcription	Lung	lung
12	chr1:86114000-86141200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:86114000-86143600	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:86114200-86120200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:86114400-86142200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:86114400-86163200	Weak transcription	Esophagus	oesophagus
17	chr1:86115200-86123400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr1:86115200-86124800	Weak transcription	Brain Substantia Nigra	brain
19	chr1:86115200-86146800	Weak transcription	Psoas Muscle	Psoas
20	chr1:86115200-86167600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:86115400-86141000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:86115600-86120000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:86116000-86123400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:86116400-86120200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:86116400-86127000	Weak transcription	Fetal Kidney	kidney
26	chr1:86116400-86143600	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:86116400-86146200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:86116600-86120200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:86116600-86121800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:86116600-86122200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:86116600-86123600	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:86116600-86129200	Weak transcription	Aorta	Aorta
33	chr1:86116600-86142200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:86116600-86145400	Weak transcription	Fetal Stomach	stomach
35	chr1:86116800-86124600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:86117000-86165800	Weak transcription	Fetal Brain Female	brain
37	chr1:86117200-86120600	Strong transcription	Primary hematopoietic stem cells	blood
38	chr1:86117400-86120000	Strong transcription	Fetal Thymus	thymus
39	chr1:86117400-86122000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:86117400-86122400	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:86117400-86122800	Strong transcription	Dnd41	blood
42	chr1:86117400-86123200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:86117600-86172000	Weak transcription	Small Intestine	intestine
44	chr1:86117800-86120000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:86117800-86120400	Strong transcription	Liver	Liver
46	chr1:86117800-86121000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:86117800-86121000	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr1:86117800-86122200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr1:86117800-86122800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:86118000-86120000	Strong transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links