Variant report

Variant	rs1418521
Chromosome Location	chr1:57040945-57040946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10493212	0.81[AFR][1000 genomes]
rs10888981	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11206846	1.00[CEU][hapmap];0.84[YRI][hapmap]
rs11206847	1.00[AFR][1000 genomes]
rs12059747	0.85[YRI][hapmap]
rs12070247	0.85[YRI][hapmap]
rs12096715	0.93[MKK][hapmap];0.81[AFR][1000 genomes]
rs12098117	0.80[YRI][hapmap]
rs1572058	1.00[CEU][hapmap];0.81[MKK][hapmap];0.90[YRI][hapmap]
rs17114100	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17114110	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17114113	1.00[CEU][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17114115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17114126	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114133	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41446844	1.00[CEU][hapmap];0.81[MKK][hapmap];0.81[YRI][hapmap]
rs55927525	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58146416	0.89[EUR][1000 genomes]
rs59475580	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72664369	1.00[EUR][1000 genomes]
rs72664370	0.89[EUR][1000 genomes]
rs72664380	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72664390	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72664391	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72664392	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72664395	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72666448	0.89[EUR][1000 genomes]
rs72666498	0.89[EUR][1000 genomes]
rs72668306	0.89[EUR][1000 genomes]
rs7539051	0.81[MKK][hapmap];0.94[YRI][hapmap];0.82[AFR][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
rs1418521	HBG1	trans	brain	seeQTL
rs1418521	HBG2	trans	brain	seeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57029400-57042200	Weak transcription	Thymus	Thymus
2	chr1:57032400-57042400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:57032800-57041000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:57035200-57041400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:57036800-57041600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:57037200-57042400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:57037200-57042400	Weak transcription	Gastric	stomach
8	chr1:57038000-57043400	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr1:57038000-57043800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:57038200-57041000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
11	chr1:57038200-57042400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:57038200-57042400	Weak transcription	Esophagus	oesophagus
13	chr1:57038400-57043200	Weak transcription	Spleen	Spleen
14	chr1:57039000-57041400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:57039000-57042000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:57039000-57042400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:57039000-57042600	Active TSS	Psoas Muscle	Psoas
18	chr1:57039200-57041200	Weak transcription	Aorta	Aorta
19	chr1:57039200-57041600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:57039200-57042400	Active TSS	Stomach Smooth Muscle	stomach
21	chr1:57039400-57041000	Active TSS	Colonic Mucosa	Colon
22	chr1:57039400-57041200	Weak transcription	Stomach Mucosa	stomach
23	chr1:57039400-57041400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:57039400-57041600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:57039400-57042400	Weak transcription	Hela-S3	cervix
26	chr1:57039600-57042000	Weak transcription	Fetal Intestine Large	intestine
27	chr1:57039600-57042200	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:57039600-57042200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr1:57039600-57042200	Weak transcription	Fetal Heart	heart
30	chr1:57039600-57042400	Active TSS	Rectal Smooth Muscle	rectum
31	chr1:57039600-57043200	Active TSS	NHLF	lung
32	chr1:57039600-57046000	Active TSS	Right Atrium	heart
33	chr1:57040000-57041400	Flanking Active TSS	Liver	Liver
34	chr1:57040000-57042400	Active TSS	Fetal Kidney	kidney
35	chr1:57040000-57042600	Active TSS	Fetal Brain Female	brain
36	chr1:57040000-57042600	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr1:57040000-57042800	Enhancers	Primary B cells from peripheral blood	blood
38	chr1:57040000-57045600	Active TSS	Brain Angular Gyrus	brain
39	chr1:57040000-57046000	Active TSS	Ovary	ovary
40	chr1:57040200-57041000	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr1:57040200-57042400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:57040200-57042400	Weak transcription	Lung	lung
43	chr1:57040200-57042800	Enhancers	Primary B cells from cord blood	blood
44	chr1:57040200-57042800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:57040200-57042800	Active TSS	Fetal Muscle Leg	muscle
46	chr1:57040200-57043400	Active TSS	Placenta	Placenta
47	chr1:57040200-57043600	Active TSS	Fetal Muscle Trunk	muscle
48	chr1:57040200-57043800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:57040200-57044200	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr1:57040200-57045800	Active TSS	Pancreatic Islets	Pancreatic Islet

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