Variant report

Variant	rs12749549
Chromosome Location	chr1:158025411-158025412
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12049103	0.82[CHB][hapmap]
rs12561890	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17454196	0.90[CHB][hapmap]
rs1925029	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971186	0.82[CHB][hapmap]
rs4971187	0.81[CHB][hapmap]
rs7527735	0.82[CHB][hapmap]
rs7530900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912640	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823720	chr1:157978556-158034017	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv999542	chr1:158015715-158368132	Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1005196	chr1:158015996-158065522	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv523208	chr1:158022217-158088687	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv526592	chr1:158024499-158026539	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1003592	chr1:158024499-158061043	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:157997600-158047600	Weak transcription	Dnd41	blood
2	chr1:158001200-158047400	Weak transcription	Thymus	Thymus
3	chr1:158013600-158025600	Weak transcription	Brain Germinal Matrix	brain
4	chr1:158013800-158027000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:158015200-158036400	Weak transcription	Esophagus	oesophagus
6	chr1:158015600-158029800	Weak transcription	Gastric	stomach
7	chr1:158016000-158025600	Weak transcription	Fetal Thymus	thymus
8	chr1:158016000-158025800	Weak transcription	Pancreas	Pancrea
9	chr1:158016200-158025600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:158016200-158025600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:158016200-158030200	Weak transcription	Fetal Intestine Small	intestine
12	chr1:158016600-158028400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:158016800-158028000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:158016800-158028600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:158016800-158029200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:158017600-158025600	Weak transcription	Right Ventricle	heart
17	chr1:158019800-158025600	Weak transcription	Aorta	Aorta
18	chr1:158020200-158028400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:158020200-158034800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:158020400-158026000	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:158020400-158026000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:158021400-158025600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:158021600-158026200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:158021800-158026600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:158022800-158029000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:158023400-158026000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:158023400-158035400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:158023600-158025600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:158023600-158026800	Weak transcription	HSMM	muscle
30	chr1:158023600-158035000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:158023600-158036600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:158023600-158036800	Weak transcription	NH-A	brain
33	chr1:158023600-158048800	Weak transcription	A549	lung
34	chr1:158023800-158025600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:158023800-158025600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:158023800-158028000	Weak transcription	NHDF-Ad	bronchial
37	chr1:158023800-158033400	Weak transcription	HSMMtube	muscle
38	chr1:158024000-158025800	Strong transcription	NHEK	skin
39	chr1:158024200-158027000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:158024200-158027800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:158024200-158029800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:158024200-158030200	Strong transcription	HMEC	breast
43	chr1:158024400-158025600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:158024400-158025600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:158024400-158025800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:158024400-158025800	Strong transcription	Hela-S3	cervix
47	chr1:158024400-158026000	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr1:158024400-158026200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:158024400-158027800	Strong transcription	Osteobl	bone
50	chr1:158024400-158033800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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