Variant report

Variant	rs1996296
Chromosome Location	chr2:78768381-78768382
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:78760713..78763886-chr2:78766006..78769531,4	K562	blood:
2	chr2:78758175..78760513-chr2:78766795..78770172,4	K562	blood:
3	chr2:78767623..78771004-chr2:78771071..78774505,4	K562	blood:
4	chr2:78748455..78750783-chr2:78766208..78769872,3	K562	blood:
5	chr2:78764342..78767175-chr2:78767388..78769753,3	K562	blood:
6	chr2:78637554..78639977-chr2:78766787..78768860,2	K562	blood:
7	chr2:78749283..78751187-chr2:78766195..78769118,2	K562	blood:

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10496206	0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1119593	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1157602	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12464108	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12466660	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12469042	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12471690	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12476863	0.95[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12477072	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12477341	0.89[CHD][hapmap]
rs1378430	0.86[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1455388	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1516246	0.85[EUR][1000 genomes]
rs1516248	0.95[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1516249	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1521500	1.00[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1521507	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1521510	0.83[CHB][hapmap]
rs1543140	0.91[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1606995	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17015321	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.93[EUR][1000 genomes]
rs17015335	0.95[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17015356	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17015360	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17015366	0.95[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17015370	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17015382	0.95[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17015396	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17015416	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1829123	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1913989	0.95[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2102995	0.84[AMR][1000 genomes]
rs2861612	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4133550	0.95[CEU][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4853389	0.95[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4853390	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4853395	0.90[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4853396	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4853397	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55819663	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56037092	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56797598	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58487153	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59189165	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60239279	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60704835	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62166571	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6717888	0.95[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6726060	0.95[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6739457	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6759775	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72808866	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72808870	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72808875	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72808881	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72808888	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72808889	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72808890	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72808891	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72808892	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72808894	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72808901	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72808902	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72810606	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72810609	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72810615	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72810645	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72810649	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72810650	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72810651	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73943117	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73943118	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7565549	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7592399	0.91[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7604707	0.91[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7607586	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7607664	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9678751	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9752363	0.89[EUR][1000 genomes]
rs9753252	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014232	chr2:78413760-79034119	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535788	chr2:78413760-79034119	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916498	chr2:78429997-79340383	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv582273	chr2:78432494-78978011	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1014484	chr2:78504497-78972453	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3584761	chr2:78545020-79430628	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv998961	chr2:78574081-79150087	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1002687	chr2:78575186-78943679	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv535790	chr2:78575186-78943679	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv874362	chr2:78582650-78805852	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv428052	chr2:78615333-79075603	Enhancers ZNF genes & repeats Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv874364	chr2:78640246-78857870	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1007043	chr2:78653616-78796446	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv874365	chr2:78658280-78805852	Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv874366	chr2:78658280-78857870	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv874367	chr2:78658280-78945755	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv874368	chr2:78668935-78805852	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv874369	chr2:78668935-78818453	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv874370	chr2:78668935-79013457	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv1004668	chr2:78673888-78797459	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv535791	chr2:78673888-78797459	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	nsv874371	chr2:78714978-78805852	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	nsv458396	chr2:78743121-78782764	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
24	nsv582289	chr2:78743121-78782764	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
25	nsv582290	chr2:78755686-78818453	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
26	nsv874372	chr2:78756804-78857870	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1996296	LRRTM4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:78764200-78769200	Active TSS	K562	blood
2	chr2:78767000-78769600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:78767200-78769200	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr2:78767400-78769000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr2:78767600-78769400	Bivalent/Poised TSS	HepG2	liver

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