Variant report

Variant	rs2517432
Chromosome Location	chr6:30945005-30945006
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30944611..30947980-chr6:30949919..30952952,3	K562	blood:
2	chr6:30944607..30947300-chr6:30955990..30958422,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SFTA2-14	chr6:30942738-30945589	NONHSAT108707

Variant related genes	Relation type
ENSG00000204544	Chromatin interaction

Extended variants
information (count: 140 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs2108775	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2248481	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2249168	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2252921	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2252925	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2252926	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2253417	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2255625	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2255626	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2255719	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2256514	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2263299	0.99[ASN][1000 genomes]
rs2263300	0.99[ASN][1000 genomes]
rs2263301	0.99[ASN][1000 genomes]
rs2263302	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2263303	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2263304	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2263305	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2263306	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2394857	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2429295	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2508016	0.83[AMR][1000 genomes]
rs2508019	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2508020	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517400	0.83[AMR][1000 genomes]
rs2517401	0.83[AMR][1000 genomes]
rs2517402	0.83[AMR][1000 genomes]
rs2517406	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2517409	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2517411	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2517412	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2517415	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2517416	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2517418	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517419	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517420	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517421	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517422	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517424	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517426	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517428	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517430	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517434	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517435	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517436	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517437	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517439	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517441	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517442	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2517444	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517445	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517446	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517447	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523907	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2523908	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2523910	0.81[AMR][1000 genomes]
rs2523911	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2523912	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2523913	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2523915	0.83[AMR][1000 genomes]
rs2523916	0.83[AMR][1000 genomes]
rs2523918	0.83[AMR][1000 genomes]
rs2523920	0.83[AMR][1000 genomes]
rs2523921	0.83[AMR][1000 genomes]
rs2523924	0.83[AMR][1000 genomes]
rs2523925	0.83[AMR][1000 genomes]
rs2523926	0.83[AMR][1000 genomes]
rs2523927	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2523928	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2523929	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2523930	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2530688	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2530689	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2530690	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2530691	0.83[AMR][1000 genomes]
rs2530694	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2530695	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2530697	0.83[AMR][1000 genomes]
rs2530698	0.83[AMR][1000 genomes]
rs2530699	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2530700	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2530701	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2530702	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2530703	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2530705	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2530706	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2530708	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2530716	0.83[AMR][1000 genomes]
rs2530717	0.83[AMR][1000 genomes]
rs2530718	0.80[AMR][1000 genomes]
rs2532919	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2844666	0.83[AMR][1000 genomes]
rs2844667	0.83[AMR][1000 genomes]
rs2844671	0.85[AMR][1000 genomes]
rs2844673	0.86[AMR][1000 genomes]
rs2844675	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2844676	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2844678	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844679	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844682	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844684	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844685	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844686	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844687	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844688	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844689	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844690	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844691	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844692	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844693	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844694	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3131928	0.81[ASN][1000 genomes]
rs3131929	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3131930	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs380808	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs41287842	0.87[AFR][1000 genomes]
rs436376	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6914559	0.81[AMR][1000 genomes]
rs7765796	0.83[AMR][1000 genomes]
rs7766113	0.83[AMR][1000 genomes]
rs9262315	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9262445	0.83[AMR][1000 genomes]
rs9262446	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9262450	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9262451	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9262456	0.83[AMR][1000 genomes]
rs9262458	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1031677	chr6:30857542-30972865	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv462743	chr6:30905313-30957766	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv601483	chr6:30905313-30957766	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv462744	chr6:30920890-30955681	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv601484	chr6:30920890-30955681	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	esv3358044	chr6:30940552-31000175	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	esv1805090	chr6:30942284-30966453	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1023108	chr6:30944982-30990490	Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30932200-30949800	Weak transcription	Right Atrium	heart
2	chr6:30933000-30950200	Weak transcription	Gastric	stomach
3	chr6:30940600-30949800	Weak transcription	Esophagus	oesophagus
4	chr6:30943200-30949800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:30944200-30945800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:30944200-30949800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:30944400-30945200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:30944400-30949600	Weak transcription	Stomach Mucosa	stomach
9	chr6:30944400-30949800	Weak transcription	H9 Cell Line	embryonic stem cell

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