Variant report

Variant	rs13161895
Chromosome Location	chr5:179471201-179471202
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179469293..179473403-chr5:179473812..179477504,5	MCF-7	breast:
2	chr5:179461642..179463908-chr5:179470350..179472207,2	K562	blood:
3	chr5:179466042..179468757-chr5:179469985..179473584,3	K562	blood:
4	chr5:179469780..179472209-chr5:179474467..179476576,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1102191	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1103811	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs12519642	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12654148	0.88[AMR][1000 genomes]
rs12656814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13166286	0.91[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs13179406	0.92[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17079966	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17079968	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs248318	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs248320	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs27012	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs27018	1.00[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34027780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34603792	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34674199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35135297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35592104	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35608303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35973843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35988237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3719	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs379655	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3797763	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3797764	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs394616	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4129403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4235504	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs438050	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4389651	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs442181	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4700853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs594202	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6873781	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6873994	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6876648	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71613436	0.91[AFR][1000 genomes]
rs71613437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71613438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs857187	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs857188	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs864481	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs864482	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
LDL cholesterol	21347282	GWAS catalog

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:179451200-179477200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:179461800-179483600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:179462800-179474800	Weak transcription	Fetal Heart	heart
5	chr5:179462800-179477000	Weak transcription	Colonic Mucosa	Colon
6	chr5:179463600-179472800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:179463600-179473400	Weak transcription	HUVEC	blood vessel
8	chr5:179463600-179475600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:179463800-179477000	Weak transcription	Small Intestine	intestine
10	chr5:179463800-179479200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr5:179463800-179482200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr5:179464400-179473200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:179464400-179473400	Weak transcription	Spleen	Spleen
14	chr5:179464400-179476800	Weak transcription	HepG2	liver
15	chr5:179464400-179477200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr5:179464600-179472400	Weak transcription	Placenta	Placenta
17	chr5:179464600-179473600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr5:179464600-179473800	Weak transcription	Right Ventricle	heart
19	chr5:179464600-179474400	Weak transcription	Primary T cells from cord blood	blood
20	chr5:179464800-179473200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:179464800-179473800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr5:179464800-179483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:179465200-179472800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:179465200-179473400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr5:179465200-179474800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:179465200-179474800	Weak transcription	Psoas Muscle	Psoas
27	chr5:179465200-179475800	Weak transcription	HSMMtube	muscle
28	chr5:179465400-179471800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:179465400-179472200	Weak transcription	Fetal Stomach	stomach
30	chr5:179465400-179472400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr5:179465400-179472800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr5:179465400-179473200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr5:179465400-179473400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr5:179465400-179473400	Weak transcription	Primary B cells from cord blood	blood
35	chr5:179465400-179473600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:179465400-179474600	Weak transcription	Lung	lung
37	chr5:179465400-179477200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr5:179465400-179484200	Weak transcription	Aorta	Aorta
39	chr5:179465600-179474800	Weak transcription	Fetal Muscle Leg	muscle
40	chr5:179467200-179472200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:179467400-179473000	Weak transcription	Brain Germinal Matrix	brain
42	chr5:179467400-179474600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr5:179467400-179474800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr5:179467400-179483200	Weak transcription	HSMM	muscle
45	chr5:179467600-179472800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:179467600-179473000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr5:179467600-179473600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr5:179467600-179473600	Weak transcription	Colon Smooth Muscle	Colon
49	chr5:179467600-179474800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr5:179467600-179474800	Weak transcription	Fetal Muscle Trunk	muscle

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