Variant report

Variant	rs2001741
Chromosome Location	chr15:52309625-52309626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51914606..51918105-chr15:52309438..52311518,3	K562	blood:
2	chr15:52259207..52267788-chr15:52308373..52314434,24	MCF-7	breast:
3	chr15:52308069..52314807-chr15:52359242..52376066,34	MCF-7	breast:
4	chr15:52262145..52266701-chr15:52309209..52314377,19	MCF-7	breast:
5	chr1:149857624..149859887-chr15:52308865..52312483,3	MCF-7	breast:
6	chr15:52262263..52265564-chr15:52309489..52315686,9	K562	blood:
7	chr15:52309194..52314432-chr15:52385325..52393461,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259712	Chromatin interaction
ENSG00000259178	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000166477	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000242327	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000104093	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10152141	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518675	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12324384	0.83[EUR][1000 genomes]
rs12324807	0.83[EUR][1000 genomes]
rs13379854	0.83[EUR][1000 genomes]
rs16964694	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16964700	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16964705	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16964720	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17540338	0.81[ASN][1000 genomes]
rs17612255	0.88[ASN][1000 genomes]
rs17612326	0.81[ASN][1000 genomes]
rs2017967	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2246726	0.91[ASN][1000 genomes]
rs2306793	1.00[EUR][1000 genomes]
rs2414120	0.88[ASN][1000 genomes]
rs2414123	0.93[ASN][1000 genomes]
rs2441779	0.91[ASN][1000 genomes]
rs2470593	0.91[ASN][1000 genomes]
rs2470594	0.91[ASN][1000 genomes]
rs2470595	0.93[ASN][1000 genomes]
rs2554340	0.88[ASN][1000 genomes]
rs2899484	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3099571	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4375608	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4456445	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4774606	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4775993	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4775995	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4775996	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55705935	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55714716	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs55873482	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56307802	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56677715	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58000475	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58936667	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61546369	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177328	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7359204	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74013636	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013638	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74013640	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74013641	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74013642	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74013644	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013645	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013646	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013647	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013648	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013653	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs74013654	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013656	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74013657	0.88[ASN][1000 genomes]
rs74013659	0.81[ASN][1000 genomes]
rs74013661	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7497554	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs751560	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8027276	0.83[EUR][1000 genomes]
rs8033365	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8033840	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8036048	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8040728	0.82[ASN][1000 genomes]
rs8041281	0.91[ASN][1000 genomes]
rs9796534	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047260	chr15:52257100-52337418	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS 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	48 gene(s)	inside rSNPs	diseases
2	nsv1050664	chr15:52265723-52342101	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv1536	chr15:52276293-52320919	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv530681	chr15:52297253-52390470	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52299400-52310800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:52299600-52310200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:52299600-52310600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr15:52299600-52310800	Weak transcription	HSMMtube	muscle
5	chr15:52301400-52310800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:52301400-52310800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:52301400-52310800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:52301400-52310800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:52303600-52310800	Weak transcription	Pancreas	Pancrea
10	chr15:52303600-52310800	Weak transcription	Right Atrium	heart
11	chr15:52303800-52310400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr15:52303800-52310600	Weak transcription	Osteobl	bone
13	chr15:52304400-52310400	Weak transcription	NHLF	lung
14	chr15:52304400-52310600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:52304400-52310800	Weak transcription	Fetal Muscle Leg	muscle
16	chr15:52304400-52310800	Weak transcription	Left Ventricle	heart
17	chr15:52304400-52310800	Weak transcription	Lung	lung
18	chr15:52304400-52310800	Weak transcription	Psoas Muscle	Psoas
19	chr15:52304400-52310800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr15:52304600-52310400	Weak transcription	NH-A	brain
21	chr15:52304600-52310800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:52304600-52310800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:52304600-52310800	Weak transcription	Brain Germinal Matrix	brain
24	chr15:52304600-52310800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr15:52304800-52310400	Weak transcription	HepG2	liver
26	chr15:52304800-52310600	Weak transcription	Adipose Nuclei	Adipose
27	chr15:52304800-52310600	Weak transcription	Brain Angular Gyrus	brain
28	chr15:52304800-52310800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr15:52304800-52310800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:52304800-52310800	Weak transcription	Brain Anterior Caudate	brain
31	chr15:52304800-52310800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr15:52304800-52310800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:52304800-52310800	Weak transcription	Brain Substantia Nigra	brain
34	chr15:52305600-52310600	Weak transcription	Colon Smooth Muscle	Colon
35	chr15:52305800-52310600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:52306000-52309800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:52306000-52309800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:52306000-52310400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr15:52306000-52310600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:52306000-52310600	Weak transcription	HSMM	muscle
41	chr15:52306000-52310600	Weak transcription	HUVEC	blood vessel
42	chr15:52306000-52310600	Weak transcription	NHDF-Ad	bronchial
43	chr15:52306200-52310600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:52306200-52310600	Weak transcription	A549	lung
45	chr15:52306200-52310600	Weak transcription	NHEK	skin
46	chr15:52306200-52310800	Weak transcription	Primary T cells from cord blood	blood
47	chr15:52306400-52310600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:52306400-52310600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr15:52306400-52310600	Weak transcription	Hela-S3	cervix
50	chr15:52306400-52310600	Weak transcription	HMEC	breast

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