Variant report

Variant	rs28549775
Chromosome Location	chr15:59121557-59121558
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59113243..59114882-chr15:59120105..59122940,2	K562	blood:
2	chr15:59120343..59122757-chr15:59124220..59126695,3	K562	blood:
3	chr15:59120109..59122005-chr15:59204966..59206971,2	K562	blood:

Variant related genes	Relation type
ENSG00000137776	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11071397	0.80[ASN][1000 genomes]
rs11631799	0.82[AFR][1000 genomes]
rs12437928	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12438114	0.92[EUR][1000 genomes]
rs12439632	0.80[ASN][1000 genomes]
rs12594276	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12595057	0.82[ASN][1000 genomes]
rs12900320	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12901817	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12914164	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1678977	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2620360	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28394222	0.80[ASN][1000 genomes]
rs28412567	0.80[ASN][1000 genomes]
rs28533385	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28537903	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs28812884	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34362744	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs347112	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34880782	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774311	0.81[AMR][1000 genomes]
rs4775095	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs481309	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs500057	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs501165	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs510759	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs556256	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs561903	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs574683	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs596094	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs597112	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs601795	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs624536	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs625312	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs652193	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs654857	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs654870	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs664936	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs684505	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs688343	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7164844	0.81[AMR][1000 genomes]
rs7170538	0.81[AMR][1000 genomes]
rs7171198	0.81[AMR][1000 genomes]
rs7178970	0.81[AMR][1000 genomes]
rs7183900	0.91[AFR][1000 genomes]
rs8029301	0.82[ASN][1000 genomes]
rs8032298	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9744045	0.81[AMR][1000 genomes]
rs9788674	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv1826703	chr15:59005922-59213678	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1798487	chr15:59027139-59213678	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv428638	chr15:59032300-59126567	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
6	nsv1035640	chr15:59105360-59190930	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59064600-59145600	Weak transcription	Gastric	stomach
2	chr15:59065800-59142800	Weak transcription	Aorta	Aorta
3	chr15:59067000-59157800	Weak transcription	Hela-S3	cervix
4	chr15:59075000-59139800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:59077800-59122000	Weak transcription	Brain Substantia Nigra	brain
6	chr15:59077800-59153600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr15:59086200-59125800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:59086400-59125800	Weak transcription	Right Ventricle	heart
9	chr15:59090200-59156600	Weak transcription	Small Intestine	intestine
10	chr15:59090400-59121600	Weak transcription	Fetal Heart	heart
11	chr15:59094200-59122800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr15:59095200-59156800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:59100400-59122200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr15:59100400-59139800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr15:59102000-59126400	Weak transcription	Stomach Mucosa	stomach
16	chr15:59103200-59135200	Weak transcription	Pancreas	Pancrea
17	chr15:59103600-59148800	Weak transcription	A549	lung
18	chr15:59103800-59122000	Weak transcription	Colon Smooth Muscle	Colon
19	chr15:59103800-59133000	Weak transcription	Spleen	Spleen
20	chr15:59103800-59157000	Weak transcription	Psoas Muscle	Psoas
21	chr15:59104000-59122200	Weak transcription	Brain Angular Gyrus	brain
22	chr15:59104000-59122400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:59104000-59122600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr15:59104000-59125200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:59104000-59125600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr15:59104000-59126800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr15:59104000-59137600	Weak transcription	Liver	Liver
28	chr15:59104000-59139800	Weak transcription	Fetal Lung	lung
29	chr15:59104000-59146600	Weak transcription	NH-A	brain
30	chr15:59104000-59148400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr15:59104000-59157000	Weak transcription	Esophagus	oesophagus
32	chr15:59104000-59157200	Weak transcription	NHLF	lung
33	chr15:59105000-59139800	Weak transcription	HMEC	breast
34	chr15:59105600-59125400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:59106000-59122600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr15:59106000-59139200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr15:59106000-59139600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr15:59106000-59156800	Weak transcription	Lung	lung
39	chr15:59106200-59137200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr15:59106200-59156800	Weak transcription	Ovary	ovary
41	chr15:59106200-59157000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:59106400-59125400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr15:59106400-59139400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr15:59106600-59122600	Weak transcription	Brain Hippocampus Middle	brain
45	chr15:59106600-59137600	Weak transcription	Fetal Muscle Trunk	muscle
46	chr15:59106600-59146400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:59106600-59157000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:59106800-59122600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr15:59106800-59125200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr15:59106800-59125400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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