Variant report

Variant	rs2288342
Chromosome Location	chr15:44854785-44854786
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:44847042..44849926-chr15:44851201..44855099,4	K562	blood:
2	chr15:44847812..44849395-chr15:44853158..44855099,2	K562	blood:
3	chr15:44848559..44851098-chr15:44853192..44855099,2	MCF-7	breast:
4	chr15:44854365..44856027-chr15:44860182..44862727,2	K562	blood:

Variant related genes	Relation type
ENSG00000259659	Chromatin interaction
ENSG00000104131	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10152710	0.94[EUR][1000 genomes]
rs1021800	0.94[EUR][1000 genomes]
rs10467977	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12324194	0.89[ASN][1000 genomes]
rs12324710	0.86[ASN][1000 genomes]
rs12591178	1.00[EUR][1000 genomes]
rs12591581	0.94[EUR][1000 genomes]
rs12591811	0.94[EUR][1000 genomes]
rs12592995	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12593125	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12593325	0.94[EUR][1000 genomes]
rs12593686	0.94[EUR][1000 genomes]
rs12593943	0.94[EUR][1000 genomes]
rs12594110	0.94[EUR][1000 genomes]
rs12594167	1.00[EUR][1000 genomes]
rs12594621	0.94[EUR][1000 genomes]
rs12594645	0.94[EUR][1000 genomes]
rs12594746	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12594905	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12594910	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12595484	0.94[EUR][1000 genomes]
rs17551416	0.94[EUR][1000 genomes]
rs2055061	1.00[EUR][1000 genomes]
rs2288341	0.94[EUR][1000 genomes]
rs2303577	0.94[EUR][1000 genomes]
rs2303578	0.87[EUR][1000 genomes]
rs2412883	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2412909	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2433350	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2555353	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2556562	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2556566	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2556567	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28508235	0.94[EUR][1000 genomes]
rs28561508	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2899113	0.94[EUR][1000 genomes]
rs2899119	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35555389	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3784565	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3784567	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3809471	1.00[EUR][1000 genomes]
rs3816928	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3986142	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3986143	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4415978	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4477677	1.00[EUR][1000 genomes]
rs4577056	1.00[EUR][1000 genomes]
rs57270586	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58956090	1.00[EUR][1000 genomes]
rs59230801	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59891213	0.85[ASN][1000 genomes]
rs60003667	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60238894	0.85[ASN][1000 genomes]
rs60399672	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61185650	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61234123	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61258861	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61278540	0.94[EUR][1000 genomes]
rs61329003	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61501839	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7162671	0.94[EUR][1000 genomes]
rs7162802	0.94[EUR][1000 genomes]
rs7163287	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7163529	0.94[EUR][1000 genomes]
rs7164709	0.94[EUR][1000 genomes]
rs7165017	0.82[ASN][1000 genomes]
rs7166278	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7166945	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7167752	0.94[EUR][1000 genomes]
rs7167870	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7169333	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7170248	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7172106	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7175200	0.94[EUR][1000 genomes]
rs7178318	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7179390	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7179894	0.94[EUR][1000 genomes]
rs7181772	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7183109	0.89[EUR][1000 genomes]
rs73417597	0.89[ASN][1000 genomes]
rs8023453	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8024623	0.94[EUR][1000 genomes]
rs8024805	0.94[EUR][1000 genomes]
rs8025727	0.94[EUR][1000 genomes]
rs8025876	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8025955	0.94[EUR][1000 genomes]
rs8026945	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8027036	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8028509	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8032079	0.94[EUR][1000 genomes]
rs883943	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9672237	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9673085	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9806511	0.86[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	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
2	esv3386433	chr15:44654644-45037538	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	135 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44830400-44855200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:44830400-44855200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:44831000-44856800	Weak transcription	Fetal Brain Male	brain
4	chr15:44833800-44857200	Weak transcription	Small Intestine	intestine
5	chr15:44838400-44857200	Weak transcription	Stomach Mucosa	stomach
6	chr15:44840000-44856000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:44840200-44858000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr15:44840600-44855600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:44840600-44857000	Strong transcription	Hela-S3	cervix
10	chr15:44842000-44951600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:44842400-44856600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr15:44842400-44857400	Weak transcription	Right Atrium	heart
13	chr15:44842800-44855800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:44842800-44856400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:44842800-44857000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:44843000-44856600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr15:44843000-44857200	Strong transcription	NH-A	brain
18	chr15:44843200-44855200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:44843200-44856200	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr15:44843200-44857000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:44843200-44857000	Strong transcription	Dnd41	blood
22	chr15:44843200-44857400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:44843200-44857400	Strong transcription	Liver	Liver
24	chr15:44843200-44857400	Strong transcription	Fetal Intestine Large	intestine
25	chr15:44843200-44857600	Strong transcription	Adipose Nuclei	Adipose
26	chr15:44843200-44867800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:44843200-44868000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:44843400-44856400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr15:44843400-44856600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:44843400-44856800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:44843600-44856200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:44843600-44866000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:44843800-44857000	Strong transcription	Primary B cells from cord blood	blood
34	chr15:44843800-44857000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr15:44843800-44857000	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr15:44843800-44857200	Strong transcription	Duodenum Mucosa	Duodenum
37	chr15:44843800-44857400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr15:44843800-44867600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr15:44844000-44857200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:44844000-44857200	Strong transcription	Fetal Muscle Leg	muscle
41	chr15:44844000-44866400	Strong transcription	Placenta	Placenta
42	chr15:44844000-44867600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:44844000-44867600	Strong transcription	Fetal Muscle Trunk	muscle
44	chr15:44844000-44868200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr15:44844000-44870400	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr15:44844200-44861800	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr15:44844400-44856800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:44844600-44857400	Strong transcription	Brain Substantia Nigra	brain
49	chr15:44844600-44867400	Strong transcription	Stomach Smooth Muscle	stomach
50	chr15:44844600-44867600	Strong transcription	Rectal Mucosa Donor 31	rectum

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