Variant report

Variant	rs4660957
Chromosome Location	chr1:47188150-47188151
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47068203..47069866-chr1:47187301..47190738,3	MCF-7	breast:
2	chr1:47183535..47186131-chr1:47187640..47190217,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159658	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10890412	0.89[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10890413	0.97[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11211334	1.00[ASW][hapmap];0.89[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11211339	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11211340	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11211351	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1139759	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12029031	0.89[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12038572	0.98[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12048954	0.89[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs12118483	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12138338	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12142631	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12733214	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1440484	0.98[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2007344	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2275380	1.00[ASW][hapmap];0.89[CEU][hapmap];0.97[GIH][hapmap];0.86[LWK][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3737729	0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4660950	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active 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 miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4660957	SLC6A9	cis	parietal	SCAN
rs4660957	LEPRE1	cis	parietal	SCAN
rs4660957	C1orf210	cis	cerebellum	SCAN
rs4660957	ATPAF1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47185200-47189600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:47185200-47189800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:47185600-47188400	Weak transcription	Psoas Muscle	Psoas
4	chr1:47185600-47190600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:47185600-47190600	Weak transcription	Brain Anterior Caudate	brain
6	chr1:47185800-47188400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:47185800-47188600	Weak transcription	Adipose Nuclei	Adipose
8	chr1:47185800-47190200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:47185800-47190200	Weak transcription	Lung	lung
10	chr1:47185800-47190200	Weak transcription	Right Ventricle	heart
11	chr1:47185800-47190200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:47185800-47190400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:47185800-47190400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:47185800-47190400	Weak transcription	Left Ventricle	heart
15	chr1:47185800-47190400	Weak transcription	HepG2	liver
16	chr1:47185800-47190600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:47185800-47190600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:47185800-47190600	Weak transcription	Brain Angular Gyrus	brain
19	chr1:47185800-47190600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:47185800-47190600	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:47185800-47190600	Weak transcription	Fetal Lung	lung
22	chr1:47185800-47190600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:47185800-47190600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:47185800-47190600	Weak transcription	Hela-S3	cervix
25	chr1:47185800-47190600	Weak transcription	HMEC	breast
26	chr1:47185800-47190600	Weak transcription	NHEK	skin
27	chr1:47185800-47190800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr1:47185800-47190800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:47185800-47194000	Weak transcription	Fetal Intestine Small	intestine
30	chr1:47185800-47194200	Weak transcription	Right Atrium	heart
31	chr1:47186000-47190600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:47186800-47188400	Enhancers	K562	blood
33	chr1:47188000-47190600	Weak transcription	Stomach Mucosa	stomach
34	chr1:47188000-47190800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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