Variant report

Variant	rs1778548
Chromosome Location	chr1:247459503-247459504
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1057996	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732300	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10924980	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10924984	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1192835	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1192836	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12239714	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846406	1.00[EUR][1000 genomes]
rs1771919	1.00[EUR][1000 genomes]
rs1771923	1.00[CEU][hapmap]
rs1771928	1.00[EUR][1000 genomes]
rs1771944	1.00[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771945	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771946	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778534	1.00[CEU][hapmap]
rs1891074	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793288	1.00[EUR][1000 genomes]
rs2799179	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4501868	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4925535	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56322743	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57178323	1.00[EUR][1000 genomes]
rs61276550	1.00[EUR][1000 genomes]
rs6657577	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669714	1.00[EUR][1000 genomes]
rs6671690	1.00[EUR][1000 genomes]
rs6676056	1.00[EUR][1000 genomes]
rs6689651	1.00[EUR][1000 genomes]
rs74152973	0.91[EUR][1000 genomes]
rs74152980	1.00[EUR][1000 genomes]
rs74152988	1.00[EUR][1000 genomes]
rs74152993	1.00[EUR][1000 genomes]
rs7517006	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs947174	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
3	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
5	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247449200-247462000	Weak transcription	Primary T cells from cord blood	blood
2	chr1:247449400-247460800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:247449600-247462400	Weak transcription	Brain Angular Gyrus	brain
4	chr1:247451000-247460800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:247451600-247460400	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:247452400-247460800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:247452600-247460800	Weak transcription	Brain Germinal Matrix	brain
8	chr1:247452600-247461200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:247452800-247462000	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:247453000-247460800	Weak transcription	Fetal Brain Female	brain
11	chr1:247453000-247462000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:247453200-247460400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:247453400-247462000	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:247453400-247463000	Weak transcription	Brain Substantia Nigra	brain
15	chr1:247454200-247462600	Weak transcription	Pancreas	Pancrea
16	chr1:247454400-247461800	Enhancers	Fetal Thymus	thymus
17	chr1:247454800-247459800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr1:247455000-247460000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:247455000-247470400	Weak transcription	Fetal Brain Male	brain
20	chr1:247455200-247460000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:247455200-247460200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:247455200-247461000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:247455200-247463000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr1:247455400-247459800	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr1:247455400-247461200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:247455600-247462600	Enhancers	H9 Cell Line	embryonic stem cell
27	chr1:247455800-247459800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:247455800-247460800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:247455800-247462200	Enhancers	H1 Cell Line	embryonic stem cell
30	chr1:247455800-247462600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:247455800-247464200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:247456000-247462000	Weak transcription	Lung	lung
33	chr1:247456000-247493400	Weak transcription	Right Atrium	heart
34	chr1:247456200-247460800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:247456200-247462200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:247456600-247471400	Weak transcription	Fetal Heart	heart
37	chr1:247456800-247462000	Weak transcription	Ovary	ovary
38	chr1:247456800-247462200	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr1:247456800-247462400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:247457000-247459800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:247457000-247460400	Weak transcription	Fetal Stomach	stomach
42	chr1:247457000-247465000	Weak transcription	Hela-S3	cervix
43	chr1:247457800-247463200	Weak transcription	Placenta	Placenta
44	chr1:247457800-247466000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:247458000-247461600	Weak transcription	Aorta	Aorta
46	chr1:247458000-247466800	Weak transcription	HSMMtube	muscle
47	chr1:247458200-247462000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:247458200-247462200	Weak transcription	HSMM	muscle
49	chr1:247458200-247462400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:247458200-247463000	Weak transcription	Muscle Satellite Cultured Cells	--

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