Variant report

Variant	rs6180
Chromosome Location	chr5:42719239-42719240
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:42710379..42715980-chr5:42716772..42720517,5	K562	blood:
2	chr5:42714480..42717427-chr5:42718299..42720344,4	K562	blood:
3	chr5:42718003..42720870-chr5:43094182..43097027,2	K562	blood:

Variant related genes	Relation type
ENSG00000112964	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10038477	0.93[YRI][hapmap]
rs10044169	0.93[YRI][hapmap]
rs10061833	0.93[YRI][hapmap]
rs10074740	0.96[YRI][hapmap]
rs10077296	0.93[YRI][hapmap]
rs1074263	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10805665	0.83[YRI][hapmap]
rs10941591	0.80[ASN][1000 genomes]
rs10941592	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10941593	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12517008	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12519532	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12521615	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs13167366	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1345824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1345825	0.95[ASN][1000 genomes]
rs1423653	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1423656	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1593071	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1862628	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1862629	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1862630	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1895457	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2014958	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2113088	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs230807	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs230812	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs230813	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs230814	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs230816	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs230819	0.95[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.92[ASN][1000 genomes]
rs230820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2459629	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2910851	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2910855	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2910856	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2910862	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2910864	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2910871	0.95[ASN][1000 genomes]
rs2910875	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap]
rs2910878	0.93[YRI][hapmap]
rs2910880	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2910881	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972756	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972757	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972758	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972759	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972761	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972763	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972767	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972780	0.93[YRI][hapmap]
rs2972783	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972992	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2972994	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2972998	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972999	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973000	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973001	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973006	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973011	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2973018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2973023	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2973028	0.93[ASN][1000 genomes]
rs2973029	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973031	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34443829	0.80[ASN][1000 genomes]
rs34502855	0.86[EUR][1000 genomes]
rs34742008	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35293842	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4242119	0.83[YRI][hapmap];0.88[AFR][1000 genomes]
rs4273617	0.86[YRI][hapmap]
rs4866800	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4866801	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4866802	0.82[ASN][1000 genomes]
rs4866948	0.93[YRI][hapmap]
rs6179	1.00[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs62370950	0.82[ASN][1000 genomes]
rs62370952	0.82[ASN][1000 genomes]
rs62370955	0.81[ASN][1000 genomes]
rs6882333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs719756	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs722677	0.97[EUR][1000 genomes]
rs9637794	0.82[ASN][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	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1029933	chr5:42611976-42833385	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537735	chr5:42611976-42833385	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	25429064	GWAS catalog

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42688400-42722200	Weak transcription	Pancreas	Pancrea
2	chr5:42706000-42720400	Weak transcription	Colon Smooth Muscle	Colon
3	chr5:42708800-42722800	Strong transcription	Liver	Liver
4	chr5:42714200-42721200	Weak transcription	Psoas Muscle	Psoas
5	chr5:42716600-42722000	Weak transcription	HSMMtube	muscle
6	chr5:42717400-42720600	Weak transcription	Fetal Kidney	kidney
7	chr5:42718000-42720400	Weak transcription	Brain Substantia Nigra	brain
8	chr5:42718000-42721000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:42718400-42719800	Enhancers	Osteobl	bone
10	chr5:42718400-42722400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr5:42718400-42722400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:42718600-42719400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:42718600-42719400	Enhancers	Primary B cells from peripheral blood	blood
14	chr5:42718600-42719400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr5:42718600-42719400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:42718600-42719400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr5:42718600-42719400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:42718600-42719400	Strong transcription	Fetal Intestine Large	intestine
19	chr5:42718600-42719600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:42718600-42719600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:42718600-42719600	Strong transcription	Fetal Muscle Trunk	muscle
22	chr5:42718600-42719600	Strong transcription	Fetal Muscle Leg	muscle
23	chr5:42718600-42719600	Strong transcription	Ovary	ovary
24	chr5:42718600-42719600	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr5:42718600-42719600	Strong transcription	Stomach Smooth Muscle	stomach
26	chr5:42718600-42719600	Enhancers	HMEC	breast
27	chr5:42718600-42719600	Enhancers	HSMM	muscle
28	chr5:42718600-42719600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr5:42718600-42719600	Enhancers	NH-A	brain
30	chr5:42718600-42719800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:42718600-42719800	Enhancers	Primary T cells fromperipheralblood	blood
32	chr5:42718600-42719800	Enhancers	Primary hematopoietic stem cells	blood
33	chr5:42718600-42719800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:42718600-42719800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr5:42718600-42719800	Strong transcription	Aorta	Aorta
36	chr5:42718600-42719800	Strong transcription	Fetal Lung	lung
37	chr5:42718600-42719800	Strong transcription	Left Ventricle	heart
38	chr5:42718600-42720400	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr5:42718600-42720800	Strong transcription	Adipose Nuclei	Adipose
40	chr5:42718600-42721000	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr5:42718600-42721200	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr5:42718600-42721800	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr5:42718800-42719400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr5:42718800-42719400	Enhancers	Thymus	Thymus
45	chr5:42718800-42719600	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr5:42718800-42719600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr5:42718800-42719600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr5:42718800-42719600	Strong transcription	Fetal Stomach	stomach
49	chr5:42718800-42719800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr5:42719000-42719400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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