Variant report

Variant	rs2944259
Chromosome Location	chr1:180784878-180784879
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180774509..180777910-chr1:180782465..180785620,3	K562	blood:
2	chr1:180784477..180786044-chr1:180786070..180788805,2	MCF-7	breast:
3	chr1:180511395..180514188-chr1:180783985..180786756,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10914096	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs11800333	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11812056	0.82[EUR][1000 genomes]
rs12085097	0.80[EUR][1000 genomes]
rs1339768	0.84[CEU][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs1970404	0.90[EUR][1000 genomes]
rs2331626	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs2331753	0.92[MEX][hapmap]
rs2331886	0.84[CEU][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs2944262	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3002113	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3002114	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs3002115	1.00[CHB][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3002116	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3002117	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs3002121	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs3002123	0.94[CEU][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes]
rs3013633	0.90[EUR][1000 genomes]
rs3013634	0.90[EUR][1000 genomes]
rs3789366	0.84[CEU][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs3843278	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs3845406	0.84[CEU][hapmap]
rs3856058	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs3903981	0.92[MEX][hapmap]
rs3908502	0.92[MEX][hapmap]
rs4083591	0.84[CEU][hapmap]
rs4108558	0.92[EUR][1000 genomes]
rs66520411	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659049	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs6659368	0.88[EUR][1000 genomes]
rs6682974	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67780680	0.93[EUR][1000 genomes]
rs72707408	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72723045	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514404	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs7524547	0.89[EUR][1000 genomes]
rs7536392	0.86[CHB][hapmap]
rs7548318	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7550031	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9425881	0.94[CEU][hapmap];0.90[EUR][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	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2944259	MR1	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180713000-180814200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:180755400-180803800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:180755400-180820400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:180756800-180810200	Weak transcription	Fetal Brain Male	brain
5	chr1:180758000-180804000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:180759000-180794800	Weak transcription	Fetal Intestine Small	intestine
7	chr1:180761200-180789200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:180761400-180794000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr1:180761400-180796400	Weak transcription	HMEC	breast
10	chr1:180761400-180804600	Weak transcription	Aorta	Aorta
11	chr1:180762000-180785200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:180763600-180806800	Weak transcription	Psoas Muscle	Psoas
13	chr1:180767400-180820400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:180767600-180795400	Weak transcription	Thymus	Thymus
15	chr1:180768000-180812000	Weak transcription	Pancreas	Pancrea
16	chr1:180769000-180802000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:180771000-180813600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:180771200-180785600	Weak transcription	HUVEC	blood vessel
19	chr1:180772000-180789400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:180772000-180789400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:180772000-180823200	Weak transcription	Fetal Stomach	stomach
22	chr1:180772200-180801800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:180773000-180799800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:180773000-180802200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:180773400-180849200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:180773800-180796600	Weak transcription	Spleen	Spleen
27	chr1:180773800-180853200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:180774000-180806800	Weak transcription	Placenta	Placenta
29	chr1:180774200-180785000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:180774400-180785800	Weak transcription	Esophagus	oesophagus
31	chr1:180774400-180797200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:180775000-180787400	Weak transcription	GM12878-XiMat	blood
33	chr1:180775000-180794000	Weak transcription	NH-A	brain
34	chr1:180775000-180831600	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:180775600-180796400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:180776400-180798400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:180776400-180801800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:180776600-180790400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr1:180776600-180801800	Weak transcription	Dnd41	blood
40	chr1:180777600-180795800	Weak transcription	A549	lung
41	chr1:180778400-180789400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:180778400-180789600	Weak transcription	Fetal Brain Female	brain
43	chr1:180778400-180790200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:180778400-180794200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:180778400-180799400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:180778600-180805600	Weak transcription	Brain Germinal Matrix	brain
47	chr1:180779000-180807400	Weak transcription	Right Ventricle	heart
48	chr1:180779800-180850800	Weak transcription	Small Intestine	intestine
49	chr1:180780000-180801600	Weak transcription	Brain Angular Gyrus	brain
50	chr1:180780200-180785200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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