Variant report

Variant	rs7497554
Chromosome Location	chr15:52349774-52349775
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52309859..52315433-chr15:52338782..52357079,28	MCF-7	breast:
2	chr15:52348651..52350159-chr15:52350189..52352122,2	K562	blood:
3	chr15:52310181..52316125-chr15:52344513..52354209,17	MCF-7	breast:
4	chr15:52263875..52265376-chr15:52348380..52350458,2	MCF-7	breast:
5	chr15:52348523..52350823-chr15:52362331..52364029,2	MCF-7	breast:
6	chr15:52348774..52350850-chr15:52362227..52365104,3	MCF-7	breast:
7	chr15:52347158..52349875-chr15:52357794..52360368,2	K562	blood:

Variant related genes	Relation type
ENSG00000259438	Chromatin interaction
ENSG00000166477	Chromatin interaction
ENSG00000069956	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10152141	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10518675	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12324384	0.83[EUR][1000 genomes]
rs12324807	0.83[EUR][1000 genomes]
rs12443497	0.82[CHB][hapmap]
rs13379854	0.83[EUR][1000 genomes]
rs16964694	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16964700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16964705	0.93[ASN][1000 genomes]
rs16964720	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17540338	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17612255	0.87[ASN][1000 genomes]
rs17612326	0.90[ASN][1000 genomes]
rs2001741	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2017967	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2246726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2306793	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414123	0.93[ASN][1000 genomes]
rs2441779	0.81[ASN][1000 genomes]
rs2470593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2470594	0.81[ASN][1000 genomes]
rs2470595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2899484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3099571	0.86[EUR][1000 genomes]
rs4375608	0.86[ASN][1000 genomes]
rs4456445	0.86[ASN][1000 genomes]
rs4491448	1.00[JPT][hapmap]
rs4774606	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4775995	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4775996	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4775997	1.00[CHB][hapmap];0.91[YRI][hapmap]
rs55705935	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55714716	0.88[ASN][1000 genomes]
rs55873482	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56307802	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56677715	0.90[ASN][1000 genomes]
rs58000475	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58936667	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61546369	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7177328	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs732097	0.82[CHB][hapmap]
rs7359204	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74013636	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74013638	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74013640	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74013641	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74013642	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74013644	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013645	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013646	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013647	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013648	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013653	0.93[ASN][1000 genomes]
rs74013654	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74013657	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs74013659	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74013661	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs751560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8027276	0.83[EUR][1000 genomes]
rs8033365	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8033840	0.95[ASN][1000 genomes]
rs8036048	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041281	0.81[ASN][1000 genomes]
rs9796534	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52314400-52359800	Weak transcription	Fetal Brain Male	brain
2	chr15:52332600-52350800	Weak transcription	Aorta	Aorta
3	chr15:52332600-52361800	Weak transcription	Gastric	stomach
4	chr15:52333000-52350800	Weak transcription	Right Ventricle	heart
5	chr15:52333000-52351000	Weak transcription	Spleen	Spleen
6	chr15:52334000-52361400	Weak transcription	Small Intestine	intestine
7	chr15:52334600-52357200	Weak transcription	Fetal Heart	heart
8	chr15:52334800-52350200	Weak transcription	Psoas Muscle	Psoas
9	chr15:52335400-52350800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:52335400-52350800	Weak transcription	Pancreas	Pancrea
11	chr15:52337600-52360600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:52337800-52357000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:52338200-52351000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr15:52339200-52351000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr15:52339200-52351200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr15:52339200-52351600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr15:52339400-52359200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:52339600-52357000	Strong transcription	Fetal Intestine Large	intestine
19	chr15:52340200-52362200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr15:52340400-52349800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr15:52341600-52357600	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr15:52341800-52358000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:52343000-52349800	Strong transcription	Fetal Muscle Leg	muscle
24	chr15:52343000-52359400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr15:52343200-52350000	Strong transcription	Fetal Stomach	stomach
26	chr15:52343200-52352000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr15:52343200-52352000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:52344200-52356600	Strong transcription	Primary T cells from cord blood	blood
29	chr15:52344400-52357200	Strong transcription	Left Ventricle	heart
30	chr15:52344600-52350800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:52344600-52362000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr15:52345000-52350400	Weak transcription	Brain Germinal Matrix	brain
33	chr15:52345000-52350800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr15:52345000-52351000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr15:52345000-52357200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr15:52345000-52357800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:52345000-52358600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr15:52345200-52350800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr15:52345200-52358000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr15:52345600-52351000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr15:52345600-52351000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr15:52345600-52352600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:52345600-52358000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:52345600-52358800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:52345600-52358800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:52345800-52359200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr15:52346200-52359000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr15:52346400-52357200	Strong transcription	NHEK	skin
49	chr15:52346600-52350800	Weak transcription	Thymus	Thymus
50	chr15:52347000-52357600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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