Variant report

Variant	rs35797812
Chromosome Location	chr12:59715982-59715983
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC16A7-4	chr12:59714688-59717255	NONHSAT029042

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11830159	0.86[EUR][1000 genomes]
rs11832063	0.85[EUR][1000 genomes]
rs11833678	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11835273	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11837506	0.86[EUR][1000 genomes]
rs12228724	0.87[ASN][1000 genomes]
rs12810255	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12810352	0.90[EUR][1000 genomes]
rs12810370	0.93[EUR][1000 genomes]
rs12812247	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12812349	0.89[EUR][1000 genomes]
rs12812654	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12815892	0.86[EUR][1000 genomes]
rs12816795	0.90[ASN][1000 genomes]
rs12817396	0.85[EUR][1000 genomes]
rs12823449	0.87[EUR][1000 genomes]
rs12824894	0.93[EUR][1000 genomes]
rs12824908	0.87[EUR][1000 genomes]
rs12831896	0.89[EUR][1000 genomes]
rs17122285	0.81[EUR][1000 genomes]
rs17122292	0.87[EUR][1000 genomes]
rs2203392	0.86[EUR][1000 genomes]
rs34238449	0.93[EUR][1000 genomes]
rs34418591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34531399	0.93[EUR][1000 genomes]
rs35103945	0.86[EUR][1000 genomes]
rs35337561	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35377390	0.87[EUR][1000 genomes]
rs35407860	0.93[EUR][1000 genomes]
rs35438740	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35563376	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35710665	0.87[EUR][1000 genomes]
rs35715187	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs36011226	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36094921	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4447211	0.86[EUR][1000 genomes]
rs4760270	0.89[ASN][1000 genomes]
rs56179488	0.87[EUR][1000 genomes]
rs56376003	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66861324	0.87[EUR][1000 genomes]
rs66931930	0.87[EUR][1000 genomes]
rs67042072	0.87[EUR][1000 genomes]
rs67534243	0.87[EUR][1000 genomes]
rs7134200	0.88[EUR][1000 genomes]
rs73120170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73120185	0.87[EUR][1000 genomes]
rs73121907	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7314663	0.85[EUR][1000 genomes]
rs7484879	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7487998	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7488364	0.89[ASN][1000 genomes]
rs7962767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7975333	0.93[EUR][1000 genomes]
rs982772	0.88[EUR][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	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1054961	chr12:59516659-59764209	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv541506	chr12:59516659-59764209	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv559052	chr12:59532203-59809256	Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1051696	chr12:59622403-59741106	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv899128	chr12:59636969-59766169	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv2762982	chr12:59659871-60000135	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1042271	chr12:59668468-59993468	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv559054	chr12:59671388-59735221	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv520767	chr12:59671388-59782228	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1038467	chr12:59680717-59999008	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv541507	chr12:59680717-59999008	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv1049084	chr12:59700333-59993468	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59711800-59716200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:59713400-59716000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr12:59715000-59716000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
4	chr12:59715000-59716000	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr12:59715200-59716000	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr12:59715200-59716000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr12:59715200-59716200	Enhancers	Brain Anterior Caudate	brain
8	chr12:59715200-59716200	Enhancers	Brain Hippocampus Middle	brain
9	chr12:59715200-59716400	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr12:59715200-59716400	Enhancers	Brain Angular Gyrus	brain
11	chr12:59715200-59716400	Enhancers	Brain Cingulate Gyrus	brain
12	chr12:59715200-59717000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:59715400-59716200	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr12:59715400-59716200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
15	chr12:59715400-59716200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:59715600-59716000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:59715600-59716000	Enhancers	Brain Substantia Nigra	brain
18	chr12:59715800-59716000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
19	chr12:59715800-59716400	Enhancers	Brain Germinal Matrix	brain
20	chr12:59715800-59716600	Genic enhancers	H1 Cell Line	embryonic stem cell
21	chr12:59715800-59716800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:59715800-59716800	Enhancers	Cortex derived primary cultured neurospheres	brain

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