Variant report

Variant	rs4129403
Chromosome Location	chr5:179476610-179476611
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179474703..179477479-chr5:179497677..179500173,3	K562	blood:
2	chr5:179048095..179049979-chr5:179476296..179478384,2	K562	blood:
3	chr5:179474524..179477374-chr5:179479073..179481485,2	MCF-7	breast:
4	chr5:179475261..179478154-chr5:179498153..179499999,2	MCF-7	breast:
5	chr5:179469293..179473403-chr5:179473812..179477504,5	MCF-7	breast:
6	chr5:179474733..179479669-chr5:179495487..179500173,5	K562	blood:

Variant related genes	Relation type
ENSG00000169045	Chromatin interaction
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10903246	0.81[GIH][hapmap]
rs1102191	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1103811	0.90[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap]
rs12519642	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12653944	0.81[GIH][hapmap]
rs12654148	0.88[AMR][1000 genomes]
rs12656814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13161895	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]
rs13166286	1.00[ASW][hapmap];0.92[CEU][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs13179406	0.93[CEU][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17079966	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17079968	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs248318	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs248320	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs27012	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs27018	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34027780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34603792	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34674199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35135297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35592104	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35608303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35973843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35988237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3719	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs379655	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3797763	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3797764	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs394616	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4130025	0.81[GIH][hapmap]
rs4235504	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs438050	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4389651	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs442181	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4700853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594202	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6873781	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6873994	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6876648	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71613436	0.91[AFR][1000 genomes]
rs71613437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71613438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs857187	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs857188	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs864481	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs864482	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4129403	LMAN2	cis	cerebellum	SCAN
rs4129403	RNF130	cis	parietal	SCAN

Chromatin state (count:85 , 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	chr5:179462800-179477000	Weak transcription	Colonic Mucosa	Colon
5	chr5:179463800-179477000	Weak transcription	Small Intestine	intestine
6	chr5:179463800-179479200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr5:179463800-179482200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr5:179464400-179476800	Weak transcription	HepG2	liver
9	chr5:179464400-179477200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:179464800-179483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:179465400-179477200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr5:179465400-179484200	Weak transcription	Aorta	Aorta
13	chr5:179467400-179483200	Weak transcription	HSMM	muscle
14	chr5:179467800-179479000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr5:179468200-179477400	Weak transcription	A549	lung
16	chr5:179469000-179477000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:179472400-179496600	Weak transcription	Stomach Mucosa	stomach
18	chr5:179473200-179482000	Enhancers	Brain Substantia Nigra	brain
19	chr5:179473400-179478000	Enhancers	Brain Hippocampus Middle	brain
20	chr5:179473400-179481600	Enhancers	Brain Anterior Caudate	brain
21	chr5:179473600-179477600	Enhancers	Colon Smooth Muscle	Colon
22	chr5:179473600-179478000	Enhancers	Adipose Nuclei	Adipose
23	chr5:179473600-179479000	Weak transcription	Spleen	Spleen
24	chr5:179473800-179477200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr5:179473800-179477200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:179473800-179477200	Weak transcription	Brain Germinal Matrix	brain
27	chr5:179473800-179477400	Enhancers	Fetal Brain Male	brain
28	chr5:179473800-179484000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:179473800-179488000	Weak transcription	Fetal Stomach	stomach
30	chr5:179474000-179477000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:179474000-179477400	Enhancers	Primary hematopoietic stem cells	blood
32	chr5:179474000-179484000	Enhancers	Brain Cingulate Gyrus	brain
33	chr5:179474000-179496200	Weak transcription	Primary B cells from cord blood	blood
34	chr5:179474600-179477400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr5:179474600-179477600	Enhancers	Brain Angular Gyrus	brain
36	chr5:179474600-179477800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr5:179474800-179477200	Enhancers	Fetal Heart	heart
38	chr5:179474800-179477200	Enhancers	Fetal Lung	lung
39	chr5:179474800-179477800	Enhancers	Liver	Liver
40	chr5:179474800-179478000	Enhancers	Right Atrium	heart
41	chr5:179474800-179478200	Enhancers	Psoas Muscle	Psoas
42	chr5:179474800-179478800	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr5:179475000-179476800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr5:179475000-179477600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:179475000-179478400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:179475200-179478000	Enhancers	H1 Cell Line	embryonic stem cell
47	chr5:179475200-179478200	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr5:179475200-179481600	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr5:179475400-179479400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:179475600-179476800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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