Variant report

Variant	rs7729481
Chromosome Location	chr5:89751450-89751451
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89748881..89751681-chr5:89752674..89755420,2	K562	blood:
2	chr5:89749257..89756333-chr5:89766701..89771382,10	K562	blood:
3	chr5:89750877..89753639-chr5:89767060..89768693,2	K562	blood:

Variant related genes	Relation type
ENSG00000176055	Chromatin interaction
ENSG00000113356	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10041220	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10043702	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10214167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10473934	1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10942593	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10942594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11953207	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11956418	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12516555	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13436287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303801	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28728101	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28815472	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2914674	0.84[JPT][hapmap]
rs34397682	0.94[EUR][1000 genomes]
rs3763070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3763072	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3805478	0.95[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59742368	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61610742	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6864062	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6867534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6872360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6889253	0.94[EUR][1000 genomes]
rs6889947	1.00[CEU][hapmap];0.98[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs6890115	1.00[CEU][hapmap];0.98[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs7730433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7732363	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv518131	chr5:89748142-89781594	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv882364	chr5:89748142-89808531	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89734600-89769000	Weak transcription	Pancreas	Pancrea
2	chr5:89736000-89753000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:89736400-89754400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:89736400-89767600	Weak transcription	Hela-S3	cervix
5	chr5:89736400-89768400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:89737600-89751800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:89737600-89757000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:89743800-89767800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr5:89744200-89759000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:89744400-89751600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:89744400-89768600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:89745400-89765800	Weak transcription	A549	lung
13	chr5:89746400-89765200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr5:89747400-89768600	Weak transcription	NHDF-Ad	bronchial
15	chr5:89747600-89760200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:89748000-89768400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr5:89748200-89757400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr5:89748200-89759600	Weak transcription	Primary T cells from cord blood	blood
19	chr5:89748400-89768600	Weak transcription	Adipose Nuclei	Adipose
20	chr5:89748600-89754400	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr5:89748600-89768200	Weak transcription	Osteobl	bone
22	chr5:89748800-89753000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:89749000-89754400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:89749200-89768400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:89749200-89768800	Weak transcription	Brain Germinal Matrix	brain
26	chr5:89749200-89768800	Weak transcription	Ovary	ovary
27	chr5:89749200-89769000	Weak transcription	Left Ventricle	heart
28	chr5:89749400-89767600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr5:89749400-89768600	Weak transcription	Fetal Intestine Large	intestine
30	chr5:89749800-89754000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr5:89749800-89768600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:89750000-89752600	Weak transcription	Fetal Muscle Leg	muscle
33	chr5:89750000-89754800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr5:89750200-89756600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr5:89750200-89768800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:89750400-89752600	Strong transcription	Liver	Liver
37	chr5:89750600-89752200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:89750600-89753200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr5:89750600-89755000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:89750600-89759000	Weak transcription	Lung	lung
41	chr5:89750600-89763800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr5:89750800-89751600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:89750800-89760200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr5:89750800-89768800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:89751000-89751800	Strong transcription	Fetal Intestine Small	intestine
46	chr5:89751000-89752000	Strong transcription	Fetal Stomach	stomach
47	chr5:89751200-89755200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:89751200-89758600	Weak transcription	Fetal Brain Female	brain
49	chr5:89751200-89766600	Weak transcription	Fetal Muscle Trunk	muscle
50	chr5:89751200-89769000	Weak transcription	Spleen	Spleen

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