Variant report

Variant	rs1574131
Chromosome Location	chr4:8041800-8041801
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8030886..8034532-chr4:8039153..8041983,3	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2385907	0.89[ASN][1000 genomes]
rs41514147	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4235253	0.85[CHB][hapmap]
rs4696735	0.89[ASN][1000 genomes]
rs4696737	0.86[CHB][hapmap];0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv829851	chr4:7958698-8049060	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv469779	chr4:7965253-8177646	Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	nsv482448	chr4:7965253-8177646	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
6	nsv829852	chr4:7991906-8151267	Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv878580	chr4:8012167-8045469	Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv470009	chr4:8015421-8085174	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv878581	chr4:8021592-8100272	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv878582	chr4:8023484-8047973	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv878583	chr4:8023484-8049713	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv878584	chr4:8023484-8075134	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv878585	chr4:8023484-8116202	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv878586	chr4:8023484-8148159	Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv593624	chr4:8026176-8047973	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv878587	chr4:8031471-8075134	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv878588	chr4:8034772-8070793	Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv878589	chr4:8034772-8089598	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1574131	GRPEL1	cis	parietal	SCAN
rs1574131	ACOX3	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8010600-8052000	Weak transcription	Left Ventricle	heart
2	chr4:8029800-8046600	Weak transcription	Brain Hippocampus Middle	brain
3	chr4:8031200-8052000	Weak transcription	Psoas Muscle	Psoas
4	chr4:8036200-8045000	Weak transcription	Esophagus	oesophagus
5	chr4:8037800-8045000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:8038000-8041800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:8038000-8052000	Weak transcription	Right Ventricle	heart
8	chr4:8039200-8057000	Weak transcription	Gastric	stomach
9	chr4:8039400-8052400	Weak transcription	Pancreas	Pancrea
10	chr4:8039400-8056600	Weak transcription	Aorta	Aorta
11	chr4:8039600-8042200	Enhancers	Brain Germinal Matrix	brain
12	chr4:8040000-8042000	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr4:8040200-8042000	Enhancers	Fetal Brain Male	brain
14	chr4:8040200-8043400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr4:8040400-8042400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr4:8040400-8043400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:8040600-8041800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:8040600-8041800	Enhancers	Adipose Nuclei	Adipose
19	chr4:8040600-8042000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:8040600-8042000	Enhancers	Fetal Brain Female	brain
21	chr4:8040600-8042600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr4:8040800-8042000	Enhancers	Brain Anterior Caudate	brain
23	chr4:8040800-8042000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
24	chr4:8041000-8041800	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr4:8041000-8042200	Enhancers	Colonic Mucosa	Colon
26	chr4:8041000-8043200	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr4:8041000-8043600	Enhancers	Spleen	Spleen
28	chr4:8041200-8041800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:8041200-8042600	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr4:8041200-8042800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr4:8041200-8046400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr4:8041200-8052400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:8041400-8046600	Weak transcription	Brain Angular Gyrus	brain
34	chr4:8041800-8042000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:8041800-8042200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:8041800-8049600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr4:8041800-8052000	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links