Variant report

Variant	rs28864995
Chromosome Location	chr15:58945671-58945672
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58945480..58947689-chr15:59040936..59043629,2	K562	blood:
2	chr15:58944978..58947722-chr15:58953875..58956765,2	K562	blood:

Variant related genes	Relation type
ENSG00000137845	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11071398	0.95[YRI][hapmap]
rs11638244	0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11854073	1.00[ASW][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs12439457	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12899638	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12911832	0.81[ASN][1000 genomes]
rs12912003	0.88[ASN][1000 genomes]
rs12912699	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1427281	0.87[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.99[ASN][1000 genomes]
rs1427282	0.80[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1648532	0.89[CHB][hapmap];0.86[YRI][hapmap]
rs1834747	0.97[ASN][1000 genomes]
rs2555356	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2657125	1.00[YRI][hapmap]
rs347115	0.92[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.95[YRI][hapmap]
rs347117	0.92[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs383902	0.92[ASW][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.95[YRI][hapmap]
rs387812	1.00[LWK][hapmap];0.96[MKK][hapmap];0.95[YRI][hapmap]
rs4275799	0.83[GIH][hapmap]
rs442495	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs474875	0.92[CHB][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.95[YRI][hapmap]
rs4774310	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4775086	0.85[ASW][hapmap];0.83[GIH][hapmap];0.80[MKK][hapmap]
rs4775087	0.92[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4775094	0.92[CHB][hapmap];0.89[GIH][hapmap]
rs507801	1.00[JPT][hapmap]
rs593742	0.89[GIH][hapmap]
rs605928	0.82[ASW][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs610877	0.92[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.95[YRI][hapmap]
rs6494029	1.00[LWK][hapmap];0.80[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6494035	0.88[ASN][1000 genomes]
rs6494036	0.92[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs653765	0.84[ASW][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs673813	0.90[CHB][hapmap]
rs714696	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7161889	0.92[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7163162	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7168776	0.83[AFR][1000 genomes]
rs7171818	0.81[CHB][hapmap]
rs7177678	0.84[ASW][hapmap];0.91[CEU][hapmap];0.87[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs7183336	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8032140	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8043406	0.85[GIH][hapmap];0.80[MKK][hapmap]
rs972801	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv904269	chr15:58906145-58992591	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv569602	chr15:58914326-58964437	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58891400-58959600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr15:58905000-58983200	Weak transcription	Esophagus	oesophagus
3	chr15:58905400-58971800	Weak transcription	Spleen	Spleen
4	chr15:58905600-58976400	Weak transcription	Gastric	stomach
5	chr15:58906400-58976400	Weak transcription	Small Intestine	intestine
6	chr15:58907800-58952000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:58911600-58951200	Weak transcription	Fetal Brain Male	brain
8	chr15:58911600-58958000	Weak transcription	Fetal Brain Female	brain
9	chr15:58914200-58957600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:58914600-58957000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:58917000-58959600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:58919800-58959200	Weak transcription	Brain Germinal Matrix	brain
13	chr15:58920200-58946600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:58920200-58957200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:58921000-58957600	Weak transcription	Colonic Mucosa	Colon
16	chr15:58921200-58946400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:58921200-58946600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:58921200-58946800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:58921200-58949400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:58921200-58959600	Weak transcription	Aorta	Aorta
21	chr15:58921200-58968400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr15:58921600-58946600	Weak transcription	Fetal Intestine Small	intestine
23	chr15:58921600-58959200	Weak transcription	NHLF	lung
24	chr15:58921600-58976600	Weak transcription	Right Ventricle	heart
25	chr15:58921800-58946400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr15:58921800-58947200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr15:58921800-58970400	Weak transcription	Stomach Mucosa	stomach
28	chr15:58922200-58959000	Weak transcription	HUVEC	blood vessel
29	chr15:58923400-58971800	Weak transcription	Pancreas	Pancrea
30	chr15:58923400-58982800	Weak transcription	Lung	lung
31	chr15:58923800-58947400	Weak transcription	Fetal Stomach	stomach
32	chr15:58924000-58960000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr15:58926400-58957600	Weak transcription	Brain Substantia Nigra	brain
34	chr15:58927000-58956600	Weak transcription	Ovary	ovary
35	chr15:58930000-58946600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:58931600-58946600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:58933000-58949600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr15:58933000-58987000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr15:58933200-58946600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:58933200-58947000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:58933200-58952400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr15:58933400-58946600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:58933400-58946600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr15:58933400-58946600	Weak transcription	Fetal Muscle Leg	muscle
45	chr15:58933400-58947000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr15:58933400-58949800	Weak transcription	Hela-S3	cervix
47	chr15:58933400-58954800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr15:58933400-58955600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr15:58933400-58956000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr15:58933600-58959000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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