Variant report

Variant	rs2725180
Chromosome Location	chr10:50369395-50369396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:49865954..49866714-chr10:50369332..50370327,2	MCF-7	breast:
2	chr10:50360501..50363437-chr10:50365924..50369669,5	K562	blood:
3	chr10:50349435..50351722-chr10:50368271..50370648,2	K562	blood:
4	chr10:50092244..50093034-chr10:50369173..50370169,2	MCF-7	breast:
5	chr10:50208979..50209840-chr10:50369197..50369909,3	MCF-7	breast:
6	chr10:50272836..50273384-chr10:50369356..50370222,2	MCF-7	breast:
7	chr10:50184525..50185128-chr10:50369265..50369817,2	MCF-7	breast:
8	chr10:50368282..50370394-chr10:50503941..50507857,3	K562	blood:
9	chr10:50364786..50371686-chr10:50371829..50376692,10	K562	blood:
10	chr10:50368282..50369845-chr10:50503941..50506916,2	K562	blood:
11	chr10:50363975..50366522-chr10:50367488..50370689,4	K562	blood:
12	chr10:50340460..50342159-chr10:50369270..50372220,2	K562	blood:
13	chr10:50340659..50342841-chr10:50368235..50370770,2	K562	blood:
14	chr10:50208660..50210019-chr10:50369301..50370268,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000177354	Chromatin interaction
ENSG00000204161	Chromatin interaction
ENSG00000236208	Chromatin interaction
ENSG00000172538	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10218995	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11100988	0.82[JPT][hapmap]
rs12198	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12258104	0.87[YRI][hapmap]
rs12258230	0.87[YRI][hapmap]
rs2002728	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2377953	0.87[ASN][1000 genomes]
rs2466744	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2466748	0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2466756	0.84[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2490837	0.83[ASN][1000 genomes]
rs2725183	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2725186	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2725187	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2725188	0.81[ASN][1000 genomes]
rs2725192	0.84[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2725193	0.87[ASN][1000 genomes]
rs2725200	0.83[JPT][hapmap]
rs2804933	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2804934	0.81[CHD][hapmap]
rs2804935	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2804936	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2804938	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2804942	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4317904	0.85[TSI][hapmap]
rs4319434	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.91[ASN][1000 genomes]
rs4319435	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4344406	0.83[JPT][hapmap]
rs4417190	0.83[JPT][hapmap]
rs4558091	0.83[JPT][hapmap]
rs4620641	0.83[JPT][hapmap]
rs4838446	0.83[JPT][hapmap]
rs4838447	0.83[JPT][hapmap]
rs6537499	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[ASN][1000 genomes]
rs7072243	0.83[JPT][hapmap]
rs7073645	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7083685	0.87[YRI][hapmap]
rs7094217	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.90[ASN][1000 genomes]
rs7095186	0.87[YRI][hapmap]
rs73304793	0.86[ASN][1000 genomes]
rs9418839	0.87[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	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2725180	A1CF	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50359000-50382200	Weak transcription	Left Ventricle	heart
2	chr10:50359200-50375400	Weak transcription	Right Atrium	heart
3	chr10:50359400-50373400	Weak transcription	Right Ventricle	heart
4	chr10:50359400-50374000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr10:50362200-50370600	Weak transcription	Spleen	Spleen
6	chr10:50362400-50380600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr10:50365400-50374800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:50365400-50374800	Weak transcription	Lung	lung
9	chr10:50365600-50369400	Weak transcription	Fetal Thymus	thymus
10	chr10:50366000-50373600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr10:50366200-50378200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr10:50366600-50369400	Enhancers	K562	blood
13	chr10:50366600-50369600	Weak transcription	Brain Substantia Nigra	brain
14	chr10:50366800-50369400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr10:50366800-50369400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr10:50366800-50370200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr10:50366800-50372400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr10:50366800-50375400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr10:50367400-50369600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr10:50367600-50376200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr10:50367600-50384600	Weak transcription	Dnd41	blood
22	chr10:50367800-50369400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr10:50368000-50371600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr10:50368000-50375600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr10:50368200-50369600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr10:50368200-50380800	Weak transcription	Esophagus	oesophagus
27	chr10:50368600-50369400	Strong transcription	Adipose Nuclei	Adipose
28	chr10:50368600-50372600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr10:50368800-50370600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr10:50368800-50370800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:50368800-50371000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr10:50369000-50370000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr10:50369000-50377200	Weak transcription	Brain Angular Gyrus	brain
34	chr10:50369200-50370800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links