Variant report

Variant	rs6490427
Chromosome Location	chr13:30336125-30336126
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1099277	1.00[ASN][1000 genomes]
rs12861019	1.00[ASN][1000 genomes]
rs12864739	1.00[ASN][1000 genomes]
rs12865525	1.00[ASN][1000 genomes]
rs12867537	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12868298	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12869833	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12872768	1.00[ASN][1000 genomes]
rs12874615	1.00[ASN][1000 genomes]
rs12875231	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12877107	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1327643	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1571255	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1631987	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs166760	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17073897	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17073905	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17073919	1.00[ASN][1000 genomes]
rs1747057	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1747058	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1747059	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1747060	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1747061	1.00[ASN][1000 genomes]
rs1747062	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1747063	1.00[ASN][1000 genomes]
rs17502757	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1772726	1.00[ASN][1000 genomes]
rs2009535	0.82[ASN][1000 genomes]
rs2031280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs2182775	0.82[ASN][1000 genomes]
rs2182776	0.82[ASN][1000 genomes]
rs2182777	0.82[ASN][1000 genomes]
rs2182778	0.89[EUR][1000 genomes]
rs2256122	1.00[ASN][1000 genomes]
rs2476650	1.00[ASN][1000 genomes]
rs2476651	1.00[ASN][1000 genomes]
rs2761929	1.00[ASN][1000 genomes]
rs2761930	1.00[ASN][1000 genomes]
rs2761931	1.00[ASN][1000 genomes]
rs2761932	1.00[ASN][1000 genomes]
rs2761934	1.00[ASN][1000 genomes]
rs2761936	1.00[ASN][1000 genomes]
rs278031	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs278032	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs278033	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs278035	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs278036	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs278039	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs278043	1.00[ASN][1000 genomes]
rs278047	1.00[ASN][1000 genomes]
rs2794295	1.00[ASN][1000 genomes]
rs2794296	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794297	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2794299	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794300	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3118078	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118079	0.87[ASN][1000 genomes]
rs3118080	1.00[ASN][1000 genomes]
rs34232669	1.00[ASN][1000 genomes]
rs34333613	0.93[ASN][1000 genomes]
rs35693706	1.00[ASN][1000 genomes]
rs35828457	1.00[ASN][1000 genomes]
rs36082926	1.00[ASN][1000 genomes]
rs4083609	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4142339	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4142340	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4335642	0.87[ASN][1000 genomes]
rs4379924	0.87[ASN][1000 genomes]
rs4385989	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs4399408	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611301	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4769021	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4769023	0.82[ASN][1000 genomes]
rs4769024	1.00[ASN][1000 genomes]
rs4769773	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57634252	1.00[ASN][1000 genomes]
rs58961964	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59768871	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6490428	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490431	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71427282	1.00[ASN][1000 genomes]
rs71427283	1.00[ASN][1000 genomes]
rs71434758	1.00[ASN][1000 genomes]
rs719199	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7322158	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73444211	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73444214	0.84[AMR][1000 genomes]
rs74042393	0.89[EUR][1000 genomes]
rs74044752	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7983788	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985986	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7992684	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8000607	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8001320	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8001330	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs818763	0.82[ASN][1000 genomes]
rs818764	1.00[ASN][1000 genomes]
rs912394	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9314977	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs943561	0.82[ASN][1000 genomes]
rs9508549	0.82[ASN][1000 genomes]
rs9508551	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9550492	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9551734	0.87[ASN][1000 genomes]
rs968612	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9788356	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899961	chr13:30226924-30407273	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30324600-30340400	Weak transcription	Adipose Nuclei	Adipose
2	chr13:30326600-30343200	Weak transcription	Spleen	Spleen
3	chr13:30328400-30337200	Weak transcription	Osteobl	bone
4	chr13:30328400-30340600	Weak transcription	NHLF	lung
5	chr13:30328600-30337200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr13:30328600-30341200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr13:30328800-30337200	Weak transcription	NHDF-Ad	bronchial
8	chr13:30328800-30337400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr13:30328800-30340400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr13:30328800-30340400	Weak transcription	Brain Hippocampus Middle	brain
11	chr13:30328800-30340800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr13:30328800-30347800	Weak transcription	Fetal Kidney	kidney
13	chr13:30328800-30351800	Weak transcription	NH-A	brain
14	chr13:30328800-30352600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr13:30329200-30338000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr13:30329200-30340000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr13:30329200-30340600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:30329200-30351200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr13:30330600-30355000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr13:30332200-30336200	Weak transcription	HSMMtube	muscle
21	chr13:30332800-30336400	Enhancers	Primary B cells from peripheral blood	blood
22	chr13:30333000-30340600	Weak transcription	Fetal Thymus	thymus
23	chr13:30333000-30340600	Weak transcription	Thymus	Thymus
24	chr13:30333200-30338000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr13:30333200-30338400	Weak transcription	Stomach Mucosa	stomach
26	chr13:30333200-30338800	Weak transcription	HSMM	muscle
27	chr13:30333200-30340200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr13:30333200-30340600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr13:30333200-30353800	Weak transcription	Gastric	stomach
30	chr13:30333200-30360200	Weak transcription	Pancreas	Pancrea
31	chr13:30333200-30368200	Weak transcription	Aorta	Aorta
32	chr13:30333400-30337000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr13:30333400-30337200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr13:30333400-30337400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr13:30333400-30338000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr13:30333400-30340400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr13:30333400-30340600	Weak transcription	Placenta	Placenta
38	chr13:30333400-30345800	Weak transcription	HepG2	liver
39	chr13:30333400-30357000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr13:30333600-30337800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr13:30333600-30338000	Weak transcription	Primary B cells from cord blood	blood
42	chr13:30333600-30340000	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr13:30333600-30340400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr13:30333600-30340600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr13:30333600-30376200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr13:30333800-30336400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr13:30333800-30337200	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr13:30334800-30340800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr13:30335200-30356800	Weak transcription	GM12878-XiMat	blood
50	chr13:30335400-30338000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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