Variant report

Variant	rs2381030
Chromosome Location	chr15:83741876-83741877
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83740878..83742663-chr15:83761508..83763284,2	K562	blood:
2	chr15:83734506..83738383-chr15:83739327..83743772,4	K562	blood:
3	chr15:83739821..83742746-chr15:83743126..83746658,4	MCF-7	breast:
4	chr15:83739861..83742001-chr15:83749630..83751735,2	K562	blood:
5	chr15:83734506..83739155-chr15:83740839..83743772,4	K562	blood:

Variant related genes	Relation type
ENSG00000263643	Chromatin interaction
ENSG00000064726	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10400812	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10520576	1.00[JPT][hapmap]
rs1112404	1.00[JPT][hapmap]
rs11259965	1.00[JPT][hapmap]
rs11259969	1.00[JPT][hapmap]
rs11852408	1.00[JPT][hapmap]
rs11852496	1.00[JPT][hapmap]
rs11853742	0.91[JPT][hapmap]
rs11856171	1.00[JPT][hapmap]
rs11857428	1.00[JPT][hapmap]
rs11857641	1.00[JPT][hapmap]
rs11858074	0.94[ASN][1000 genomes]
rs11858377	1.00[JPT][hapmap]
rs12439782	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12440386	1.00[JPT][hapmap]
rs12441585	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs12443109	1.00[JPT][hapmap]
rs12591855	1.00[JPT][hapmap]
rs12592391	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12593316	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12593638	0.91[JPT][hapmap]
rs12594496	1.00[JPT][hapmap]
rs12595330	1.00[JPT][hapmap]
rs12899522	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12900411	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12901811	0.94[ASN][1000 genomes]
rs12902721	0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12903066	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12904695	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12906027	0.94[ASN][1000 genomes]
rs12906626	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12907032	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12911706	0.94[ASN][1000 genomes]
rs12911891	0.94[ASN][1000 genomes]
rs12913130	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12917594	0.95[ASN][1000 genomes]
rs13329195	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13329269	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17158080	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs17158127	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17294476	0.90[JPT][hapmap]
rs17507300	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17567151	1.00[JPT][hapmap]
rs17567869	1.00[JPT][hapmap]
rs17568459	1.00[JPT][hapmap]
rs2034617	0.91[JPT][hapmap]
rs2034618	1.00[JPT][hapmap]
rs2084839	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28436027	0.91[JPT][hapmap]
rs28485801	0.95[ASN][1000 genomes]
rs28580677	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3087804	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34869943	0.90[ASN][1000 genomes]
rs35207081	0.94[ASN][1000 genomes]
rs35627116	0.95[ASN][1000 genomes]
rs36038412	0.94[ASN][1000 genomes]
rs4079029	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4563011	1.00[JPT][hapmap]
rs61375537	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6603044	0.94[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6603046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6603047	0.91[JPT][hapmap]
rs66606849	0.94[ASN][1000 genomes]
rs67482297	0.94[ASN][1000 genomes]
rs67822554	0.94[ASN][1000 genomes]
rs7163516	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7164083	0.82[JPT][hapmap]
rs7165114	1.00[JPT][hapmap]
rs7165978	1.00[JPT][hapmap]
rs7166645	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170547	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7172665	1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7173166	1.00[JPT][hapmap]
rs7177599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7180407	1.00[JPT][hapmap]
rs7181169	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7495911	1.00[JPT][hapmap]
rs750214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8023669	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs8027193	1.00[JPT][hapmap]
rs8027577	1.00[JPT][hapmap]
rs8031896	0.97[ASN][1000 genomes]
rs8035810	1.00[JPT][hapmap]
rs8037783	1.00[JPT][hapmap]
rs8038486	1.00[JPT][hapmap]
rs8040457	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040998	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8043224	1.00[JPT][hapmap]
rs9646239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs965264	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv3338509	chr15:83740748-83744946	Enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2381030	TM6SF1	cis	cerebellum	SCAN
rs2381030	WHAMM	cis	parietal	SCAN
rs2381030	WHAMM	cis	cerebellum	SCAN
rs2381030	BTBD1	cis	lymphoblastoid	seeQTL
rs2381030	BTBD1	cis	parietal	SCAN
rs2381030	ARNT2	cis	cerebellum	SCAN
rs2381030	HDGFRP3	Cis_1M	lymphoblastoid	RTeQTL
rs2381030	BTBD1	cis	Nerve Tibial	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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