Variant report

Variant	rs7412746
Chromosome Location	chr1:150860471-150860472
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	chr1:150859611..150863685-chr1:150866729..150869931,3	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 35 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1081512	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11204725	0.89[ASW][hapmap];0.89[CEU][hapmap];0.89[GIH][hapmap];0.85[LWK][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.91[YRI][hapmap]
rs11204735	0.93[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11204737	1.00[ASW][hapmap];0.93[CEU][hapmap];0.89[GIH][hapmap];0.85[LWK][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11587718	0.83[YRI][hapmap]
rs12125650	0.89[ASW][hapmap];0.93[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap]
rs12126004	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12402006	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12404199	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410050	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12568757	0.89[ASW][hapmap];0.93[CEU][hapmap];0.89[GIH][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap]
rs12758227	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1673160	0.83[YRI][hapmap]
rs1722784	0.91[YRI][hapmap]
rs2039590	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2089081	0.87[EUR][1000 genomes]
rs2305814	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs267733	0.83[YRI][hapmap]
rs3754211	0.93[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs486836	0.93[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4970926	0.89[ASW][hapmap];0.82[CEU][hapmap];0.93[MKK][hapmap]
rs4970932	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4970976	0.84[EUR][1000 genomes]
rs6587551	0.82[EUR][1000 genomes]
rs6694531	0.89[ASW][hapmap];0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
5	nsv2810	chr1:150835173-150879869	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv547844	chr1:150857555-150862767	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	esv3320702	chr1:150860090-150862929	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3320701	chr1:150860127-150862916	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv3320700	chr1:150860142-150862842	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv3320699	chr1:150860157-150862876	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv3320703	chr1:150860264-150862814	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv11698	chr1:150860288-150862841	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv547845	chr1:150860471-150862767	Enhancers Active TSS Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Melanoma	21983785	GWAS catalog

mRNA abundance (count:34)

SNP	Gene	Cis/trans	Tissue	Source
rs7412746	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs7412746	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs7412746	ARNT	cis	cerebellum	SCAN
rs7412746	CTSK	cis	parietal	SCAN
rs7412746	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs7412746	CTSS	cis	lymphoblastoid	seeQTL
rs7412746	CTSS	cis	parietal	SCAN
rs7412746	ARNT	cis	normal skin	skin_eQTL
rs7412746	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs7412746	RP11-316M1.12	cis	Artery Tibial	GTEx
rs7412746	CTSK	cis	cerebellum	SCAN
rs7412746	MCL1	cis	cerebellum	SCAN
rs7412746	FLG	cis	cerebellum	SCAN
rs7412746	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs7412746	CTSK	cis	multi-tissue	Pritchard
rs7412746	PSMD4	cis	parietal	SCAN
rs7412746	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs7412746	ARNT	cis	parietal	SCAN
rs7412746	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs7412746	ARNT	cis	uninvolved skin	skin_eQTL
rs7412746	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs7412746	HORMAD1	cis	parietal	SCAN
rs7412746	HORMAD1	cis	Esophagus Mucosa	GTEx
rs7412746	RP11-316M1.12	cis	Whole Blood	GTEx
rs7412746	RP11-316M1.12	cis	Thyroid	GTEx
rs7412746	FMO5	cis	cerebellum	SCAN
rs7412746	HORMAD1	cis	lesional skin	skin_eQTL
rs7412746	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs7412746	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs7412746	CTSK	cis	lymphoblastoid	seeQTL
rs7412746	HORMAD1	cis	Nerve Tibial	GTEx
rs7412746	HORMAD1	cis	uninvolved skin	skin_eQTL
rs7412746	RP11-316M1.12	cis	lung	GTEx
rs7412746	CTSS	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150854000-150862200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:150854600-150862600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:150856800-150861800	Weak transcription	GM12878-XiMat	blood
4	chr1:150859800-150867800	Weak transcription	Hela-S3	cervix
5	chr1:150860200-150863600	Weak transcription	Placenta	Placenta

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