Variant report

Variant	rs4775996
Chromosome Location	chr15:52344116-52344117
allele	A/G
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	chr15:52339219..52341051-chr15:52343518..52345839,3	MCF-7	breast:
3	chr15:52342647..52344200-chr15:52358974..52361107,2	MCF-7	breast:
4	chr15:52343651..52347096-chr15:52360408..52363365,3	K562	blood:
5	chr15:52316178..52317685-chr15:52342819..52344591,2	MCF-7	breast:
6	chr15:52342579..52344959-chr15:52354184..52356320,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259438	Chromatin interaction
ENSG00000069956	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10152141	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10518675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12324384	0.83[EUR][1000 genomes]
rs12324807	0.83[EUR][1000 genomes]
rs13379854	0.83[EUR][1000 genomes]
rs16964694	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[ASN][1000 genomes]
rs16964700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16964705	0.85[ASN][1000 genomes]
rs16964720	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17540338	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17612326	0.97[ASN][1000 genomes]
rs2001741	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2017967	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2246726	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs2306793	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414123	0.85[ASN][1000 genomes]
rs2470593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2470595	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2554321	1.00[GIH][hapmap]
rs2554341	1.00[GIH][hapmap]
rs2593189	1.00[GIH][hapmap]
rs2899484	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3099571	0.86[EUR][1000 genomes]
rs4375608	0.86[AMR][1000 genomes]
rs4456445	0.86[AMR][1000 genomes]
rs4491448	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4774606	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775993	0.89[AMR][1000 genomes]
rs4775995	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4775997	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs55705935	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55714716	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs55873482	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56307802	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56677715	0.83[ASN][1000 genomes]
rs58000475	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58936667	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61546369	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7177328	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs732097	0.89[CHB][hapmap]
rs7359204	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74013636	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74013638	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs74013640	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs74013641	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs74013642	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs74013644	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74013645	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74013646	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74013647	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74013648	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74013653	0.85[ASN][1000 genomes]
rs74013654	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74013656	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74013657	0.90[ASN][1000 genomes]
rs74013659	0.97[ASN][1000 genomes]
rs74013661	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7497554	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]
rs751560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8027276	0.83[EUR][1000 genomes]
rs8033365	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8033840	0.87[ASN][1000 genomes]
rs8036048	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9796534	0.86[AMR][1000 genomes];0.80[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	chr15:52312800-52345400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:52314400-52359800	Weak transcription	Fetal Brain Male	brain
3	chr15:52332400-52348200	Weak transcription	Colonic Mucosa	Colon
4	chr15:52332600-52349000	Weak transcription	Esophagus	oesophagus
5	chr15:52332600-52349400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:52332600-52350800	Weak transcription	Aorta	Aorta
7	chr15:52332600-52361800	Weak transcription	Gastric	stomach
8	chr15:52332800-52344400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:52333000-52344200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:52333000-52344400	Weak transcription	Left Ventricle	heart
11	chr15:52333000-52345400	Weak transcription	Lung	lung
12	chr15:52333000-52348200	Weak transcription	HSMMtube	muscle
13	chr15:52333000-52350800	Weak transcription	Right Ventricle	heart
14	chr15:52333000-52351000	Weak transcription	Spleen	Spleen
15	chr15:52333200-52348600	Weak transcription	Colon Smooth Muscle	Colon
16	chr15:52334000-52361400	Weak transcription	Small Intestine	intestine
17	chr15:52334600-52344200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr15:52334600-52344200	Weak transcription	Fetal Kidney	kidney
19	chr15:52334600-52357200	Weak transcription	Fetal Heart	heart
20	chr15:52334800-52350200	Weak transcription	Psoas Muscle	Psoas
21	chr15:52335000-52344200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr15:52335000-52344200	Weak transcription	Hela-S3	cervix
23	chr15:52335000-52348000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:52335400-52344200	Weak transcription	Ovary	ovary
25	chr15:52335400-52350800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:52335400-52350800	Weak transcription	Pancreas	Pancrea
27	chr15:52337600-52360600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr15:52337800-52357000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr15:52338000-52344200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr15:52338200-52344200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:52338200-52346200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:52338200-52347400	Weak transcription	Stomach Mucosa	stomach
33	chr15:52338200-52351000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr15:52338400-52344200	Weak transcription	Primary B cells from cord blood	blood
35	chr15:52338400-52344200	Weak transcription	Thymus	Thymus
36	chr15:52338400-52347400	Weak transcription	Brain Angular Gyrus	brain
37	chr15:52338600-52346800	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr15:52338800-52345800	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:52338800-52347000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr15:52339000-52344200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr15:52339000-52349000	Strong transcription	Fetal Intestine Small	intestine
42	chr15:52339200-52344200	Weak transcription	Primary T cells from cord blood	blood
43	chr15:52339200-52344200	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr15:52339200-52345000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr15:52339200-52345000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr15:52339200-52345600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr15:52339200-52348800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr15:52339200-52351000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr15:52339200-52351200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr15:52339200-52351600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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