Variant report

Variant	rs6691109
Chromosome Location	chr1:56916164-56916165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10888971	0.97[EUR][1000 genomes]
rs11206824	0.89[EUR][1000 genomes]
rs1815487	0.91[EUR][1000 genomes]
rs1889145	0.98[ASN][1000 genomes]
rs2151391	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2780857	0.97[EUR][1000 genomes]
rs55694910	0.85[EUR][1000 genomes]
rs6421496	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6588634	0.91[EUR][1000 genomes]
rs6588635	0.91[EUR][1000 genomes]
rs6670090	0.96[EUR][1000 genomes]
rs6684929	0.98[ASN][1000 genomes]
rs6693179	0.98[ASN][1000 genomes]
rs72664303	0.84[EUR][1000 genomes]
rs72664304	0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS 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 target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6691109	SLC1A7	cis	parietal	SCAN
rs6691109	CYB5RL	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56905400-56942600	Weak transcription	Gastric	stomach
2	chr1:56908400-56916800	Weak transcription	Brain Anterior Caudate	brain
3	chr1:56910000-56916200	Enhancers	Liver	Liver
4	chr1:56912000-56916200	Enhancers	Right Atrium	heart
5	chr1:56912000-56916400	Enhancers	Hela-S3	cervix
6	chr1:56912000-56916600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:56912000-56916600	Enhancers	Left Ventricle	heart
8	chr1:56912800-56918600	Weak transcription	Fetal Heart	heart
9	chr1:56912800-56922400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:56912800-56923400	Weak transcription	Spleen	Spleen
11	chr1:56913200-56917400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:56913600-56917000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:56913800-56917000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:56913800-56917200	Weak transcription	Small Intestine	intestine
15	chr1:56913800-56917400	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:56913800-56943200	Weak transcription	Aorta	Aorta
17	chr1:56914200-56916200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:56914200-56916200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr1:56914200-56916200	Enhancers	Lung	lung
20	chr1:56914200-56916200	Enhancers	Psoas Muscle	Psoas
21	chr1:56914200-56916400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr1:56914200-56917400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:56914200-56919800	Enhancers	Fetal Intestine Small	intestine
24	chr1:56914400-56919600	Enhancers	Fetal Intestine Large	intestine
25	chr1:56914600-56917800	Weak transcription	Fetal Kidney	kidney
26	chr1:56914600-56919800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr1:56914800-56916200	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr1:56914800-56916200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:56914800-56916200	Enhancers	Right Ventricle	heart
30	chr1:56914800-56916400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:56914800-56916400	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr1:56914800-56916600	Enhancers	Fetal Muscle Trunk	muscle
33	chr1:56914800-56916600	Enhancers	Fetal Muscle Leg	muscle
34	chr1:56914800-56917200	Weak transcription	Fetal Lung	lung
35	chr1:56915000-56917200	Weak transcription	Pancreas	Pancrea
36	chr1:56915000-56922400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:56915200-56917800	Weak transcription	NHDF-Ad	bronchial
38	chr1:56915200-56922400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:56915200-56935800	Weak transcription	NHLF	lung
40	chr1:56915400-56916200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr1:56915400-56916200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:56915400-56916200	Enhancers	Esophagus	oesophagus
43	chr1:56915400-56916400	Enhancers	H9 Cell Line	embryonic stem cell
44	chr1:56915400-56916600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr1:56915400-56917400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:56915400-56917600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:56915400-56918800	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr1:56915600-56916400	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr1:56915600-56917000	Weak transcription	Adipose Nuclei	Adipose
50	chr1:56915600-56919000	Enhancers	Rectal Mucosa Donor 31	rectum

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