Variant report

Variant	rs28417868
Chromosome Location	chr15:40455647-40455648
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40455615..40458970-chr15:40466942..40470330,4	K562	blood:
2	chr15:40330665..40333715-chr15:40453352..40456401,3	K562	blood:
3	chr15:40453925..40456102-chr15:40486988..40489014,2	MCF-7	breast:
4	chr15:40371657..40374195-chr15:40453312..40456256,2	K562	blood:
5	chr15:40330254..40332910-chr15:40454901..40456422,2	K562	blood:

Variant related genes	Relation type
ENSG00000140319	Chromatin interaction
ENSG00000248508	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11070254	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070255	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12102172	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12385956	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13380113	1.00[EUR][1000 genomes]
rs13380241	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1494534	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1801528	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1869906	1.00[EUR][1000 genomes]
rs28390245	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28418337	0.87[AMR][1000 genomes]
rs28485685	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28501335	1.00[EUR][1000 genomes]
rs28526743	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28561898	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28565228	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28606396	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28637656	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28637697	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28657938	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28668026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28673302	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28744626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28750294	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28792493	1.00[EUR][1000 genomes]
rs28844897	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28869227	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35611758	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56888636	1.00[EUR][1000 genomes]
rs57029027	1.00[EUR][1000 genomes]
rs58216655	1.00[EUR][1000 genomes]
rs58355728	0.87[AMR][1000 genomes]
rs58584688	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60743501	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60889301	1.00[EUR][1000 genomes]
rs7164281	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168394	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168416	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7173239	1.00[EUR][1000 genomes]
rs7178873	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73377835	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389487	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389489	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389492	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389507	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389531	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389536	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389540	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390146	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390155	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390162	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390167	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390168	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390187	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73391309	0.87[AMR][1000 genomes]
rs73391316	0.87[AMR][1000 genomes]
rs73392641	1.00[EUR][1000 genomes]
rs8023956	1.00[EUR][1000 genomes]
rs8026988	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8364	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9672591	1.00[EUR][1000 genomes]
rs967945	0.87[AMR][1000 genomes]
rs9806126	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9806144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40452600-40455800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:40453000-40456400	Active TSS	GM12878-XiMat	blood
3	chr15:40453400-40456600	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr15:40453800-40455800	Flanking Active TSS	HUVEC	blood vessel
5	chr15:40453800-40460200	Weak transcription	Right Atrium	heart
6	chr15:40453800-40474600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:40453800-40525000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:40454000-40459600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr15:40454000-40460600	Weak transcription	Placenta	Placenta
10	chr15:40454000-40471000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:40454000-40474600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:40454000-40515200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr15:40454200-40455800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:40454200-40471400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr15:40454400-40455800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:40454400-40455800	Flanking Active TSS	HepG2	liver
17	chr15:40454600-40456200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
18	chr15:40454600-40456200	Transcr. at gene 5' and 3'	K562	blood
19	chr15:40454600-40462400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr15:40454600-40463200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:40454600-40502400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr15:40454800-40456200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr15:40454800-40456600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr15:40454800-40463200	Weak transcription	Fetal Intestine Large	intestine
25	chr15:40454800-40465600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:40454800-40474400	Weak transcription	Primary B cells from cord blood	blood
27	chr15:40454800-40524200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:40455000-40455800	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr15:40455000-40455800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr15:40455000-40455800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:40455000-40456400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr15:40455000-40456400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:40455000-40457800	Weak transcription	Fetal Intestine Small	intestine
34	chr15:40455000-40474600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:40455000-40474600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:40455200-40455800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
37	chr15:40455200-40457000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr15:40455200-40461000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr15:40455200-40465800	Weak transcription	Fetal Kidney	kidney
40	chr15:40455400-40455800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:40455400-40455800	Active TSS	NH-A	brain
42	chr15:40455400-40456200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr15:40455400-40456600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr15:40455400-40456800	Weak transcription	Fetal Stomach	stomach
45	chr15:40455400-40457000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr15:40455400-40457200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr15:40455400-40457200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr15:40455400-40457200	Weak transcription	Fetal Heart	heart
49	chr15:40455400-40457200	Weak transcription	NHDF-Ad	bronchial
50	chr15:40455400-40457200	Weak transcription	NHLF	lung

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