Variant report

Variant	rs893379
Chromosome Location	chr15:93194688-93194689
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:93191617..93195403-chr15:93257490..93261490,4	MCF-7	breast:
2	chr15:93191674..93195100-chr15:93197023..93199781,4	K562	blood:

Variant related genes	Relation type
ENSG00000185442	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12443091	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496712	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16974307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs184048	0.80[EUR][1000 genomes]
rs2254142	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs2453901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285754	0.89[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs285755	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs285757	0.89[CEU][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs285758	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs285766	0.80[CEU][hapmap];0.83[MEX][hapmap];0.80[EUR][1000 genomes]
rs285772	0.96[EUR][1000 genomes]
rs366789	0.82[EUR][1000 genomes]
rs373481	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs406032	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413450	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434826	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs503112	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6496969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178546	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
3	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
5	nsv1040501	chr15:93177153-93286393	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs893379	PRC1	cis	parietal	SCAN
rs893379	RGMA	cis	parietal	SCAN
rs893379	HIST1H2AH	trans	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93171000-93197400	Weak transcription	Primary T cells from cord blood	blood
2	chr15:93182000-93197800	Weak transcription	Small Intestine	intestine
3	chr15:93182600-93197200	Weak transcription	Fetal Kidney	kidney
4	chr15:93183200-93198400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:93187600-93195800	Weak transcription	Brain Angular Gyrus	brain
6	chr15:93187800-93195600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:93189000-93195600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr15:93189000-93197000	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:93189200-93195200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr15:93189200-93195400	Weak transcription	Right Ventricle	heart
11	chr15:93189400-93197000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:93189400-93197000	Weak transcription	Esophagus	oesophagus
13	chr15:93190600-93197000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:93190800-93195400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:93191000-93196600	Weak transcription	HSMM	muscle
16	chr15:93191000-93197400	Weak transcription	HSMMtube	muscle
17	chr15:93191800-93195400	Weak transcription	Fetal Intestine Small	intestine
18	chr15:93192000-93195400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:93192000-93196800	Weak transcription	Liver	Liver
20	chr15:93192000-93197400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:93192400-93195400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:93192800-93195600	Weak transcription	HUVEC	blood vessel
23	chr15:93193000-93195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr15:93193000-93195200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr15:93193000-93196200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:93193400-93195000	ZNF genes & repeats	GM12878-XiMat	blood
27	chr15:93193600-93194800	Enhancers	Placenta	Placenta
28	chr15:93193800-93195400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr15:93193800-93195400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr15:93193800-93199000	Enhancers	Fetal Heart	heart
31	chr15:93194000-93195000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:93194000-93195000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:93194000-93195000	ZNF genes & repeats	Fetal Muscle Leg	muscle
34	chr15:93194000-93195200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr15:93194000-93195200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr15:93194000-93195400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:93194000-93195400	Weak transcription	Stomach Mucosa	stomach
38	chr15:93194000-93195600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr15:93194000-93196800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:93194000-93197200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr15:93194000-93197400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr15:93194200-93194800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
43	chr15:93194200-93195400	Weak transcription	Fetal Stomach	stomach
44	chr15:93194200-93195400	Weak transcription	Left Ventricle	heart
45	chr15:93194200-93195400	Weak transcription	Lung	lung
46	chr15:93194200-93195400	Weak transcription	Pancreas	Pancrea
47	chr15:93194200-93195600	Weak transcription	Fetal Lung	lung
48	chr15:93194200-93195600	Weak transcription	Gastric	stomach
49	chr15:93194200-93195600	Weak transcription	Right Atrium	heart
50	chr15:93194200-93197000	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links