Variant report

Variant	rs1877158
Chromosome Location	chr1:226242772-226242773
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226219248..226223033-chr1:226239868..226243673,3	MCF-7	breast:
2	chr1:226235405..226240206-chr1:226241102..226244494,5	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10157179	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10753411	0.96[CEU][hapmap];0.83[CHB][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs10799333	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10799334	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10915920	0.83[EUR][1000 genomes]
rs10915921	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10915923	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10915924	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs10915927	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915932	0.81[AFR][1000 genomes]
rs11576089	0.82[ASN][1000 genomes]
rs12128917	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2001307	0.91[EUR][1000 genomes]
rs4271181	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs4477241	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4604663	0.94[EUR][1000 genomes]
rs4653438	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653439	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653703	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653704	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653705	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653706	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4653707	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6426096	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6426098	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426099	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6675606	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6682659	0.96[CEU][hapmap];0.83[CHB][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6693325	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6701318	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73100558	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7550220	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7553984	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9701639	0.82[AMR][1000 genomes];0.97[EUR][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	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription 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	65 gene(s)	inside rSNPs	diseases
2	nsv524575	chr1:226234883-226242772	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
3	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1877158	H3F3A	cis	Nerve Tibial	GTEx
rs1877158	H3F3A	cis	Esophagus Mucosa	GTEx
rs1877158	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs1877158	H3F3A	cis	Artery Tibial	GTEx
rs1877158	FBXO28	cis	cerebellum	SCAN
rs1877158	MOSC1	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226222600-226248600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:226226000-226248000	Weak transcription	Left Ventricle	heart
3	chr1:226229600-226248200	Weak transcription	Brain Germinal Matrix	brain
4	chr1:226229800-226249400	Weak transcription	Spleen	Spleen
5	chr1:226230000-226249200	Weak transcription	Aorta	Aorta
6	chr1:226231200-226249200	Weak transcription	Pancreas	Pancrea
7	chr1:226232000-226249200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:226232200-226249400	Weak transcription	Gastric	stomach
9	chr1:226232600-226248600	Weak transcription	Brain Substantia Nigra	brain
10	chr1:226234600-226243400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:226234600-226248000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:226234600-226248800	Weak transcription	HSMM	muscle
13	chr1:226234800-226248800	Weak transcription	HSMMtube	muscle
14	chr1:226235000-226248200	Weak transcription	Fetal Intestine Large	intestine
15	chr1:226235000-226248800	Weak transcription	Colonic Mucosa	Colon
16	chr1:226235200-226246200	Weak transcription	Fetal Lung	lung
17	chr1:226235200-226248600	Weak transcription	HepG2	liver
18	chr1:226235200-226249200	Weak transcription	Small Intestine	intestine
19	chr1:226235400-226248000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr1:226235400-226248600	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:226235400-226249200	Weak transcription	Esophagus	oesophagus
22	chr1:226235600-226243400	Weak transcription	Brain Anterior Caudate	brain
23	chr1:226235600-226248200	Weak transcription	Fetal Intestine Small	intestine
24	chr1:226235800-226246200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:226235800-226248200	Weak transcription	Stomach Mucosa	stomach
26	chr1:226236200-226248200	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:226236200-226248600	Weak transcription	Fetal Brain Male	brain
28	chr1:226236800-226248200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:226236800-226248600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:226237000-226246200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:226237200-226248600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:226237600-226246000	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:226237600-226248800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:226238400-226248200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:226238600-226249000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:226240000-226248400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:226240200-226244000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:226240600-226244200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:226240800-226247800	Weak transcription	Psoas Muscle	Psoas
40	chr1:226241000-226243400	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:226241000-226244200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr1:226241000-226249200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:226241200-226242800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr1:226241200-226248200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr1:226241400-226244400	Strong transcription	Liver	Liver
46	chr1:226241600-226244600	Strong transcription	Primary T cells from cord blood	blood
47	chr1:226241600-226246600	Strong transcription	Fetal Thymus	thymus
48	chr1:226241800-226242800	Enhancers	Ovary	ovary
49	chr1:226241800-226243000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:226241800-226244600	Strong transcription	Placenta	Placenta

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