Variant report

Variant	rs16964700
Chromosome Location	chr15:52337463-52337464
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52333359..52335753-chr15:52337024..52338910,2	MCF-7	breast:
2	chr15:52327906..52330801-chr15:52336087..52340276,6	MCF-7	breast:
3	chr15:52310424..52313443-chr15:52334748..52338325,6	MCF-7	breast:
4	chr15:52332465..52334999-chr15:52337431..52339850,2	K562	blood:
5	chr15:52316174..52318031-chr15:52336524..52338315,2	MCF-7	breast:
6	chr15:52308807..52313747-chr15:52329198..52338033,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259438	Chromatin interaction
ENSG00000069956	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10152141	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10518675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16964694	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964705	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964720	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17540338	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17612255	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17612326	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2001741	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2017967	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2246726	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2414120	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2414123	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2441779	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2470593	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2470594	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2470595	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2554340	0.86[ASN][1000 genomes]
rs2899484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3099571	0.86[ASN][1000 genomes]
rs4375608	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4456445	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4491448	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs4774606	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4775993	0.86[AMR][1000 genomes]
rs4775995	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4775996	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4775997	1.00[CHB][hapmap]
rs55705935	0.85[ASN][1000 genomes]
rs55714716	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55873482	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56307802	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs56677715	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58000475	0.90[ASN][1000 genomes]
rs58936667	0.85[ASN][1000 genomes]
rs61546369	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7177328	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs732097	0.90[CHB][hapmap]
rs7359204	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs74013636	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs74013638	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs74013640	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs74013641	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs74013642	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs74013644	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs74013645	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs74013646	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs74013647	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs74013648	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs74013653	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74013654	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs74013656	0.95[ASN][1000 genomes]
rs74013657	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013659	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74013661	0.85[ASN][1000 genomes]
rs7497554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs751560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033365	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8033840	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8036048	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8041281	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9796534	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52312800-52345400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:52314400-52359800	Weak transcription	Fetal Brain Male	brain
3	chr15:52325800-52342200	Weak transcription	HUVEC	blood vessel
4	chr15:52326800-52342800	Weak transcription	Fetal Brain Female	brain
5	chr15:52327000-52340600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:52327600-52340200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:52332400-52348200	Weak transcription	Colonic Mucosa	Colon
8	chr15:52332600-52338200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:52332600-52340400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:52332600-52342400	Weak transcription	NHDF-Ad	bronchial
11	chr15:52332600-52349000	Weak transcription	Esophagus	oesophagus
12	chr15:52332600-52349400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:52332600-52350800	Weak transcription	Aorta	Aorta
14	chr15:52332600-52361800	Weak transcription	Gastric	stomach
15	chr15:52332800-52339600	Weak transcription	Fetal Intestine Large	intestine
16	chr15:52332800-52340400	Weak transcription	Brain Germinal Matrix	brain
17	chr15:52332800-52340400	Weak transcription	Placenta	Placenta
18	chr15:52332800-52344400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr15:52333000-52337600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr15:52333000-52337600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr15:52333000-52337800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:52333000-52337800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr15:52333000-52338000	Weak transcription	Thymus	Thymus
24	chr15:52333000-52338200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:52333000-52338200	Weak transcription	Fetal Thymus	thymus
26	chr15:52333000-52338800	Weak transcription	NHLF	lung
27	chr15:52333000-52339000	Weak transcription	Fetal Intestine Small	intestine
28	chr15:52333000-52339000	Weak transcription	Fetal Lung	lung
29	chr15:52333000-52339000	Weak transcription	Fetal Muscle Leg	muscle
30	chr15:52333000-52339200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:52333000-52339400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr15:52333000-52339600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:52333000-52340200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:52333000-52340400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:52333000-52341000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr15:52333000-52341000	Weak transcription	HSMM	muscle
37	chr15:52333000-52344200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr15:52333000-52344400	Weak transcription	Left Ventricle	heart
39	chr15:52333000-52345400	Weak transcription	Lung	lung
40	chr15:52333000-52348200	Weak transcription	HSMMtube	muscle
41	chr15:52333000-52350800	Weak transcription	Right Ventricle	heart
42	chr15:52333000-52351000	Weak transcription	Spleen	Spleen
43	chr15:52333200-52337600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:52333200-52337800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr15:52333200-52338400	Weak transcription	NH-A	brain
46	chr15:52333200-52338600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr15:52333200-52339600	Weak transcription	Fetal Stomach	stomach
48	chr15:52333200-52340800	Weak transcription	Adipose Nuclei	Adipose
49	chr15:52333200-52342800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr15:52333200-52348600	Weak transcription	Colon Smooth Muscle	Colon

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