Variant report

Variant	rs270904
Chromosome Location	chr7:137356651-137356652
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AKR1D1-6	chr7:137356474-137357129	l_3488_chr7:137337580-137357129_testes

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1019583	0.87[CEU][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes]
rs1723069	0.87[EUR][1000 genomes]
rs270891	0.91[CEU][hapmap];0.86[CHB][hapmap];0.92[MEX][hapmap]
rs270893	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs270894	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs270895	0.87[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs270896	0.87[CEU][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs270897	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs270898	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs270899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs270900	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs270901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs270902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778797	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs3778798	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3800624	0.87[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3800626	0.87[CEU][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4728420	0.83[CEU][hapmap]
rs6948537	0.81[EUR][1000 genomes]
rs6976725	0.83[CEU][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes]
rs7457119	0.87[CEU][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022793	chr7:137187383-137619359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv1812888	chr7:137283212-137366467	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv464731	chr7:137356651-137404781	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
4	nsv608466	chr7:137356651-137404781	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs270904	SLC13A4	cis	cerebellum	SCAN
rs270904	ADCK2	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:137343800-137359000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:137344000-137358000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr7:137350400-137356800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:137350400-137358000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:137350600-137358000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:137351400-137357000	Enhancers	HSMMtube	muscle
7	chr7:137352000-137357000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:137352800-137356800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:137353600-137357400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr7:137354600-137357000	Enhancers	Fetal Brain Male	brain
11	chr7:137355000-137357000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:137355800-137356800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:137355800-137356800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:137355800-137356800	Weak transcription	Left Ventricle	heart
15	chr7:137355800-137357400	Enhancers	Osteobl	bone
16	chr7:137355800-137370600	Weak transcription	Aorta	Aorta
17	chr7:137356000-137361800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr7:137356200-137357800	Weak transcription	NHDF-Ad	bronchial
19	chr7:137356400-137356800	Weak transcription	Brain Anterior Caudate	brain
20	chr7:137356400-137365800	Weak transcription	HSMM	muscle
21	chr7:137356600-137357000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr7:137356600-137357000	Enhancers	Fetal Heart	heart
23	chr7:137356600-137358600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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