Variant report

Variant	rs11578535
Chromosome Location	chr1:113356094-113356095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC16A1-1	chr1:113355832-113357984	ucscGeneNc_uc001ede_1

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11102546	1.00[ASN][1000 genomes]
rs11102549	0.84[ASN][1000 genomes]
rs11102550	0.84[ASN][1000 genomes]
rs11102552	0.84[ASN][1000 genomes]
rs11102554	0.84[ASN][1000 genomes]
rs11102555	0.84[ASN][1000 genomes]
rs11102556	0.84[ASN][1000 genomes]
rs11578123	1.00[ASN][1000 genomes]
rs12066478	0.84[ASN][1000 genomes]
rs12079364	0.92[ASN][1000 genomes]
rs12081613	0.92[ASN][1000 genomes]
rs12082068	0.92[ASN][1000 genomes]
rs12082284	0.92[ASN][1000 genomes]
rs12083391	0.92[ASN][1000 genomes]
rs12083699	0.92[ASN][1000 genomes]
rs12084078	0.92[ASN][1000 genomes]
rs12085206	0.92[ASN][1000 genomes]
rs12085380	0.92[ASN][1000 genomes]
rs12086719	0.92[ASN][1000 genomes]
rs12087350	0.92[ASN][1000 genomes]
rs12088632	0.92[ASN][1000 genomes]
rs12090523	0.84[ASN][1000 genomes]
rs12092282	0.84[ASN][1000 genomes]
rs12093508	0.84[ASN][1000 genomes]
rs12094711	0.84[ASN][1000 genomes]
rs12094750	0.84[ASN][1000 genomes]
rs12097209	0.92[ASN][1000 genomes]
rs12097373	0.92[ASN][1000 genomes]
rs12741871	0.92[ASN][1000 genomes]
rs12742016	0.92[ASN][1000 genomes]
rs12754894	0.84[ASN][1000 genomes]
rs12756538	0.92[ASN][1000 genomes]
rs34186834	0.92[ASN][1000 genomes]
rs34517984	0.92[ASN][1000 genomes]
rs34789338	0.84[ASN][1000 genomes]
rs34839402	0.92[ASN][1000 genomes]
rs34889921	0.92[ASN][1000 genomes]
rs34903691	0.84[ASN][1000 genomes]
rs34915129	0.92[ASN][1000 genomes]
rs34986359	0.92[ASN][1000 genomes]
rs35086049	0.92[ASN][1000 genomes]
rs35386139	0.84[ASN][1000 genomes]
rs35603180	0.92[ASN][1000 genomes]
rs6537759	0.84[ASN][1000 genomes]
rs6537760	0.84[ASN][1000 genomes]
rs6662943	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667358	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6667856	0.84[ASN][1000 genomes]
rs6674386	0.92[ASN][1000 genomes]
rs6677225	0.92[ASN][1000 genomes]
rs6677237	0.92[ASN][1000 genomes]
rs6687010	0.92[ASN][1000 genomes]
rs6687045	0.84[ASN][1000 genomes]
rs6687054	0.92[ASN][1000 genomes]
rs6692406	0.92[ASN][1000 genomes]
rs6698018	0.92[ASN][1000 genomes]
rs6702269	0.84[ASN][1000 genomes]
rs71513997	0.92[ASN][1000 genomes]
rs71514000	0.92[ASN][1000 genomes]
rs71659377	0.92[ASN][1000 genomes]
rs71659378	0.84[ASN][1000 genomes]
rs7516867	0.84[ASN][1000 genomes]
rs7517501	0.84[ASN][1000 genomes]
rs7520778	0.84[ASN][1000 genomes]
rs7527193	0.84[ASN][1000 genomes]
rs7527283	0.84[ASN][1000 genomes]
rs7528133	0.92[ASN][1000 genomes]
rs7537461	0.92[ASN][1000 genomes]
rs7539492	0.92[ASN][1000 genomes]
rs7539588	0.92[ASN][1000 genomes]
rs7539948	0.92[ASN][1000 genomes]
rs7541584	0.92[ASN][1000 genomes]
rs7543983	0.92[ASN][1000 genomes]
rs7554350	0.92[ASN][1000 genomes]
rs9429493	0.84[ASN][1000 genomes]
rs9429494	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv818378	chr1:113263711-113434818	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv1008434	chr1:113288282-113447426	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	nsv1004102	chr1:113295805-113551210	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
12	nsv872160	chr1:113301657-113409751	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv547567	chr1:113313563-113384015	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv1000352	chr1:113350929-113405903	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
15	nsv1011519	chr1:113351374-113402040	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113342000-113361800	Weak transcription	Right Atrium	heart
2	chr1:113352200-113360400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:113352200-113360400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:113352400-113360200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:113352400-113360400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:113352400-113369200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:113353200-113361200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:113353200-113364400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:113353200-113364800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:113353400-113360400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:113353800-113357800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:113354000-113357800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:113354400-113356400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:113354400-113360400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:113354600-113358800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:113354800-113356400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:113355200-113356400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:113355200-113357800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:113355400-113356800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr1:113355600-113356200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr1:113355600-113356800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:113355600-113360400	Weak transcription	Placenta	Placenta
23	chr1:113355800-113356200	Weak transcription	K562	blood
24	chr1:113355800-113356400	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr1:113355800-113356600	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr1:113355800-113356600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:113356000-113356200	Flanking Active TSS	H9 Cell Line	embryonic stem cell
28	chr1:113356000-113356200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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