Variant report

Variant	rs2774311
Chromosome Location	chr1:114660704-114660705
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114635004..114637775-chr1:114660348..114663171,3	MCF-7	breast:
2	chr1:114657028..114661761-chr1:114663955..114667421,5	MCF-7	breast:
3	chr1:114653835..114656090-chr1:114660410..114662840,2	K562	blood:
4	chr1:114656303..114663278-chr1:114663805..114668148,7	MCF-7	breast:
5	chr1:114653590..114655647-chr1:114659608..114662763,3	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1872478	0.95[CHB][hapmap];0.94[ASN][1000 genomes]
rs2481087	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2629811	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2629812	0.88[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2774309	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2774310	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs479359	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs552581	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs588983	0.86[CHB][hapmap];0.92[CHD][hapmap];0.85[ASN][1000 genomes]
rs633255	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs659646	0.85[ASN][1000 genomes]
rs661871	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs676268	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs676715	0.92[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs676743	0.88[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs677635	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs964592	0.80[CHB][hapmap];0.85[ASN][1000 genomes]
rs964593	0.85[ASN][1000 genomes]
rs964594	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1849780	chr1:114577463-114663164	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2752948	chr1:114658958-114751958	Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2774311	DRAM2	cis	cerebellum	SCAN
rs2774311	SYCP1	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114630400-114675800	Weak transcription	Pancreas	Pancrea
2	chr1:114632200-114661000	Weak transcription	Brain Germinal Matrix	brain
3	chr1:114648800-114661600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:114649400-114661000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:114650800-114666000	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:114654800-114661600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr1:114655800-114662200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr1:114655800-114683800	Weak transcription	Right Atrium	heart
9	chr1:114656600-114661200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:114656800-114660800	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr1:114657200-114660800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:114657200-114661000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:114657200-114661600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:114657200-114661800	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr1:114657600-114665600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:114657600-114665800	Weak transcription	Brain Anterior Caudate	brain
17	chr1:114657800-114661600	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr1:114658200-114666200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:114658600-114661600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:114658800-114661200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
21	chr1:114659400-114662200	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr1:114659800-114661200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:114659800-114661400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr1:114659800-114661600	Enhancers	Fetal Muscle Leg	muscle
25	chr1:114660000-114660800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:114660000-114661400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:114660200-114677200	Weak transcription	Fetal Brain Female	brain
28	chr1:114660400-114661200	Enhancers	Fetal Stomach	stomach
29	chr1:114660400-114662000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr1:114660400-114662400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr1:114660600-114660800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:114660600-114661000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:114660600-114661200	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr1:114660600-114661400	Enhancers	Fetal Brain Male	brain
35	chr1:114660600-114661400	Enhancers	Fetal Lung	lung
36	chr1:114660600-114661400	Enhancers	Placenta	Placenta
37	chr1:114660600-114661600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:114660600-114661600	Enhancers	Primary hematopoietic stem cells	blood
39	chr1:114660600-114662000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links