Variant report

Variant	rs12030411
Chromosome Location	chr1:220871975-220871976
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1690716	0.81[EUR][1000 genomes]
rs17008307	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2960571	0.98[ASN][1000 genomes]
rs2994528	0.81[EUR][1000 genomes]
rs337180	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs364360	0.98[ASN][1000 genomes]
rs384264	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs405682	0.98[ASN][1000 genomes]
rs409286	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs413426	0.82[ASN][1000 genomes]
rs416768	0.97[ASN][1000 genomes]
rs700036	0.91[ASN][1000 genomes]
rs774128	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs774130	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468194	chr1:220845610-220885612	Bivalent Enhancer Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv549227	chr1:220845610-220885612	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv2754270	chr1:220850116-220929155	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220865200-220873200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:220865200-220874200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:220865200-220879200	Weak transcription	Ovary	ovary
4	chr1:220865400-220873200	Weak transcription	Fetal Brain Female	brain
5	chr1:220865400-220873800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:220865400-220874400	Weak transcription	Colonic Mucosa	Colon
7	chr1:220865400-220876200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:220866000-220872400	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:220866000-220873400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:220866000-220873600	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:220866600-220872400	Weak transcription	Fetal Brain Male	brain
12	chr1:220866600-220879600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:220868400-220873200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:220868400-220873600	Strong transcription	Fetal Intestine Small	intestine
15	chr1:220869800-220872000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:220869800-220872000	Genic enhancers	Placenta	Placenta
17	chr1:220869800-220872600	Strong transcription	Duodenum Mucosa	Duodenum
18	chr1:220870000-220872000	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr1:220870000-220872600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:220870000-220872800	Genic enhancers	Liver	Liver
21	chr1:220870000-220873600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:220870200-220872000	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:220870400-220872000	Strong transcription	Lung	lung
24	chr1:220870400-220872000	Strong transcription	Right Ventricle	heart
25	chr1:220870400-220873600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:220870600-220873000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:220870600-220873400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:220870600-220873600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:220870800-220872200	Genic enhancers	Fetal Intestine Large	intestine
30	chr1:220871000-220872000	Strong transcription	Fetal Stomach	stomach
31	chr1:220871200-220873600	Weak transcription	Brain Germinal Matrix	brain
32	chr1:220871400-220873000	Weak transcription	Aorta	Aorta
33	chr1:220871400-220873200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:220871400-220874000	Weak transcription	Brain Anterior Caudate	brain
35	chr1:220871400-220876200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:220871600-220872400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr1:220871600-220872400	Enhancers	A549	lung
38	chr1:220871600-220873200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:220871600-220873200	Weak transcription	Brain Angular Gyrus	brain
40	chr1:220871600-220873200	Weak transcription	Pancreas	Pancrea
41	chr1:220871600-220873400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:220871600-220873400	Weak transcription	Left Ventricle	heart
43	chr1:220871600-220878400	Weak transcription	Gastric	stomach
44	chr1:220871800-220872000	Flanking Active TSS	HepG2	liver
45	chr1:220871800-220872600	Weak transcription	Adipose Nuclei	Adipose
46	chr1:220871800-220873400	Weak transcription	Fetal Lung	lung
47	chr1:220871800-220876600	Weak transcription	Spleen	Spleen
48	chr1:220871800-220878800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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