Variant report

Variant	rs5878
Chromosome Location	chr1:173878832-173878833
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173826383..173830416-chr1:173877536..173882048,5	MCF-7	breast:
2	chr1:173834428..173840700-chr1:173878764..173885322,14	MCF-7	breast:
3	chr1:173876474..173879309-chr1:173881795..173883444,2	K562	blood:
4	chr1:173829979..173831869-chr1:173877762..173880722,2	K562	blood:
5	chr1:173872283..173875090-chr1:173876429..173879185,2	K562	blood:
6	chr1:173873481..173875734-chr1:173878715..173880288,2	K562	blood:
7	chr1:173835432..173839472-chr1:173878792..173882155,3	K562	blood:

Variant related genes	Relation type
ENSG00000234741	Chromatin interaction
ENSG00000208317	Chromatin interaction
ENSG00000185278	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10798295	0.83[ASW][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap]
rs10798301	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs10798302	0.87[CHB][hapmap]
rs12066153	0.87[CHB][hapmap]
rs12071594	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12071663	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12078824	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12563301	0.91[CHB][hapmap]
rs1322770	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1322775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1322777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1322780	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1799876	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884994	0.83[CHB][hapmap]
rs1951627	0.87[CHB][hapmap];0.88[GIH][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs2065171	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2208850	0.81[MEX][hapmap]
rs2295366	0.85[MEX][hapmap]
rs4652169	0.91[CHB][hapmap]
rs4652229	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971204	0.87[YRI][hapmap]
rs5877	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6663875	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6665484	0.87[CHB][hapmap]
rs6677660	0.87[CHB][hapmap]
rs6686083	0.87[CHB][hapmap]
rs6689285	0.87[CHB][hapmap]
rs6695327	0.87[CHB][hapmap]
rs6696163	0.87[CHB][hapmap]
rs6699146	0.91[CHB][hapmap]
rs714624	0.87[CHB][hapmap]
rs7349095	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7413166	0.86[CHB][hapmap]
rs7533430	0.95[CHB][hapmap]
rs7544605	0.85[AMR][1000 genomes]
rs7552939	0.83[ASW][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7553788	0.90[CHB][hapmap]
rs9286895	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs941989	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9425430	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9425435	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9425755	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9425756	0.85[MEX][hapmap]
rs9425765	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9425766	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9661233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs5878		cis	Lymphoblastoid	GTEx
rs5878	CENPL	cis	lymphoblastoid	seeQTL
rs5878	RABGAP1L	cis	parietal	SCAN
rs5878	PRDX6	cis	parietal	SCAN
rs5878	SNORD78	cis	parietal	SCAN
rs5878	SERPINC1	cis	multi-tissue	Pritchard
rs5878	FMO1	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173855800-173880400	Weak transcription	Thymus	Thymus
2	chr1:173856000-173883000	Weak transcription	Right Ventricle	heart
3	chr1:173856200-173880400	Weak transcription	Psoas Muscle	Psoas
4	chr1:173856400-173880000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:173856600-173881200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:173856600-173907200	Weak transcription	Brain Germinal Matrix	brain
7	chr1:173857000-173883800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:173857400-173880400	Weak transcription	Fetal Brain Female	brain
9	chr1:173857400-173881800	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:173857400-173884400	Weak transcription	HepG2	liver
11	chr1:173857400-173885800	Weak transcription	Fetal Intestine Large	intestine
12	chr1:173857400-173902000	Weak transcription	HSMMtube	muscle
13	chr1:173858200-173902800	Weak transcription	Left Ventricle	heart
14	chr1:173858600-173881400	Weak transcription	Primary B cells from cord blood	blood
15	chr1:173858600-173886800	Weak transcription	Placenta	Placenta
16	chr1:173862000-173891600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:173864600-173886600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:173869000-173880200	Weak transcription	Brain Angular Gyrus	brain
19	chr1:173869200-173880200	Weak transcription	Brain Substantia Nigra	brain
20	chr1:173870000-173880400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:173870000-173898000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:173870200-173880600	Weak transcription	Adipose Nuclei	Adipose
23	chr1:173870400-173887400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:173871200-173908400	Weak transcription	Spleen	Spleen
25	chr1:173871400-173879400	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:173872200-173880200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:173872200-173880800	Weak transcription	Fetal Stomach	stomach
28	chr1:173872400-173896200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:173873600-173880600	Weak transcription	Ovary	ovary
30	chr1:173874400-173899800	Weak transcription	Primary T cells from cord blood	blood
31	chr1:173876400-173884000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:173878400-173879200	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:173878600-173879200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:173878600-173883200	Genic enhancers	Liver	Liver
35	chr1:173878800-173879000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:173878800-173879000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:173878800-173879000	ZNF genes & repeats	Aorta	Aorta

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