Variant report

Variant	rs28479712
Chromosome Location	chr15:40364263-40364264
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40362632..40364659-chr15:40399625..40401274,2	K562	blood:
2	chr15:40359476..40364618-chr15:40393648..40401523,12	MCF-7	breast:
3	chr15:40361459..40366979-chr15:40389781..40395512,5	MCF-7	breast:
4	chr15:40355457..40358717-chr15:40360057..40366974,8	K562	blood:

Variant related genes	Relation type
ENSG00000248508	Chromatin interaction
ENSG00000104081	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11638521	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16970286	0.89[ASN][1000 genomes]
rs16970291	0.93[ASN][1000 genomes]
rs16970319	0.88[ASN][1000 genomes]
rs28361302	0.87[ASN][1000 genomes]
rs28371998	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28379715	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28534747	0.89[EUR][1000 genomes]
rs28537079	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28587891	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28605815	0.86[ASN][1000 genomes]
rs28620926	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4923852	0.83[EUR][1000 genomes]
rs4924415	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924416	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7181230	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7183977	0.90[EUR][1000 genomes]
rs9972424	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9972442	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40346000-40367400	Weak transcription	K562	blood
2	chr15:40346200-40372800	Weak transcription	Fetal Kidney	kidney
3	chr15:40348600-40365800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr15:40348800-40365400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr15:40357600-40365800	Weak transcription	Primary T cells from cord blood	blood
6	chr15:40359000-40368000	Weak transcription	Ovary	ovary
7	chr15:40359400-40364400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:40359800-40366000	Enhancers	Fetal Thymus	thymus
9	chr15:40361800-40365800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:40361800-40368400	Weak transcription	HMEC	breast
11	chr15:40362200-40364400	Weak transcription	Gastric	stomach
12	chr15:40362200-40364400	Weak transcription	HUVEC	blood vessel
13	chr15:40362200-40364800	Weak transcription	Fetal Intestine Small	intestine
14	chr15:40362200-40365800	Weak transcription	Primary B cells from cord blood	blood
15	chr15:40362200-40367600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:40362200-40367600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:40362200-40368800	Weak transcription	Osteobl	bone
18	chr15:40362200-40372600	Weak transcription	Small Intestine	intestine
19	chr15:40362200-40373000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:40362200-40373600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:40362400-40364400	Weak transcription	Brain Anterior Caudate	brain
22	chr15:40362400-40364400	Weak transcription	Brain Hippocampus Middle	brain
23	chr15:40362400-40364400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:40362400-40364400	Weak transcription	Right Atrium	heart
25	chr15:40362400-40364400	Weak transcription	NHDF-Ad	bronchial
26	chr15:40362400-40364600	Weak transcription	Brain Substantia Nigra	brain
27	chr15:40362400-40364800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr15:40362400-40365000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr15:40362400-40367400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:40362400-40367600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr15:40362400-40368000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:40362400-40369200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr15:40362400-40372800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr15:40362400-40374200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:40362600-40364400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr15:40362600-40364400	Weak transcription	Fetal Heart	heart
37	chr15:40362600-40364400	Weak transcription	Placenta	Placenta
38	chr15:40362600-40364400	Weak transcription	Left Ventricle	heart
39	chr15:40362600-40364400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr15:40362600-40364400	Weak transcription	HSMMtube	muscle
41	chr15:40362600-40364600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:40362600-40364600	Weak transcription	Adipose Nuclei	Adipose
43	chr15:40362600-40364600	Weak transcription	Colonic Mucosa	Colon
44	chr15:40362600-40365000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr15:40362600-40367200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr15:40362600-40367600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr15:40362600-40367600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr15:40362600-40367600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:40362600-40367600	Weak transcription	Spleen	Spleen
50	chr15:40362600-40367600	Weak transcription	A549	lung

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