Variant report

Variant	rs407271
Chromosome Location	chr1:76974324-76974325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10873889	0.89[ASW][hapmap]
rs315093	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6685154	0.80[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870621	chr1:76620313-76997071	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv534168	chr1:76718950-77039352	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv462006	chr1:76826279-77042405	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv546585	chr1:76826279-77042405	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv997827	chr1:76929028-77201457	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv462017	chr1:76940156-76982445	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
7	nsv546586	chr1:76940156-76982445	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	inside rSNPs	diseases
8	nsv462028	chr1:76948044-76976522	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
9	nsv546587	chr1:76948044-76976522	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
10	nsv462039	chr1:76948044-77019597	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv470718	chr1:76948044-77019597	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv546588	chr1:76948044-77019597	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv462050	chr1:76948044-77019986	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv462062	chr1:76948044-77019986	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv462073	chr1:76948044-77019986	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv546589	chr1:76948044-77019986	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
17	nsv1003826	chr1:76965331-77656929	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
18	nsv535006	chr1:76965331-77656929	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
19	nsv428774	chr1:76971045-77075766	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs407271	SLC44A5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76967200-76977000	Weak transcription	Fetal Stomach	stomach
2	chr1:76967200-76977400	Weak transcription	Primary B cells from cord blood	blood
3	chr1:76967400-76976800	Weak transcription	Fetal Kidney	kidney
4	chr1:76968200-76976600	Weak transcription	Primary T cells from cord blood	blood
5	chr1:76969600-76974800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:76969600-76974800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:76969600-76976600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:76969600-76976800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:76969600-76977000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:76969600-76977000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:76969600-76981800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:76970000-76976800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:76970400-76974600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:76970600-76981800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:76971600-76976800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:76972000-76976200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:76973800-76974400	Enhancers	Left Ventricle	heart
18	chr1:76974000-76974400	Enhancers	Aorta	Aorta
19	chr1:76974000-76976000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr1:76974200-76974600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:76974200-76976800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:76974200-76976800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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