Variant report

Variant	rs1419110
Chromosome Location	chr1:154768689-154768690
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154750627..154752191-chr1:154767353..154769437,2	MCF-7	breast:
2	chr1:154764144..154765879-chr1:154767700..154769213,2	MCF-7	breast:
3	chr1:154767709..154770416-chr1:154785808..154787544,2	MCF-7	breast:
4	chr1:154762591..154764311-chr1:154767126..154769154,2	MCF-7	breast:
5	chr1:154767850..154769379-chr1:154804804..154806305,2	K562	blood:
6	chr1:154764756..154767197-chr1:154768149..154770805,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10908440	0.85[CHD][hapmap]
rs11584635	1.00[CHB][hapmap];0.80[CHD][hapmap];0.83[ASN][1000 genomes]
rs12133662	0.88[JPT][hapmap]
rs17719312	0.85[CHD][hapmap]
rs1891806	1.00[CHB][hapmap];0.80[CHD][hapmap];0.82[ASN][1000 genomes]
rs72700254	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
3	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv470740	chr1:154568683-154796895	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS 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	18 gene(s)	inside rSNPs	diseases
5	nsv464050	chr1:154568683-154801247	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv547958	chr1:154568683-154801247	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv872452	chr1:154750989-154769561	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1419110	SNAPIN	cis	parietal	SCAN
rs1419110	EFNA3	cis	cerebellum	SCAN
rs1419110	ZNF687	cis	cerebellum	SCAN
rs1419110	CRTC2	cis	cerebellum	SCAN
rs1419110	S100A6	cis	cerebellum	SCAN
rs1419110	YY1AP1	cis	cerebellum	SCAN
rs1419110	SETDB1	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154764600-154768800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:154764600-154770000	Weak transcription	Brain Angular Gyrus	brain
3	chr1:154764600-154773800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:154764600-154778400	Weak transcription	Right Atrium	heart
5	chr1:154764600-154779400	Weak transcription	Spleen	Spleen
6	chr1:154764800-154772200	Weak transcription	Fetal Stomach	stomach
7	chr1:154764800-154782600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:154765000-154775200	Weak transcription	Brain Substantia Nigra	brain
9	chr1:154765400-154772400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:154765600-154775600	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:154765800-154775800	Weak transcription	Brain Anterior Caudate	brain
12	chr1:154767000-154769400	Weak transcription	GM12878-XiMat	blood
13	chr1:154767600-154769800	Enhancers	Fetal Thymus	thymus
14	chr1:154767800-154769800	Enhancers	Fetal Muscle Leg	muscle
15	chr1:154768200-154769600	Enhancers	Thymus	Thymus
16	chr1:154768400-154769600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr1:154768600-154769200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr1:154768600-154769400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:154768600-154769400	Enhancers	Fetal Brain Female	brain
20	chr1:154768600-154769600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:154768600-154769600	Enhancers	HMEC	breast
22	chr1:154768600-154769600	Bivalent Enhancer	NHEK	skin

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