Variant report

Variant	rs10518683
Chromosome Location	chr15:52654123-52654124
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52653880..52655772-chr15:52658306..52660812,2	K562	blood:
2	chr15:52586205..52590641-chr15:52653204..52656400,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1104800	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1108808	1.00[ASN][1000 genomes]
rs12101973	0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12913979	0.96[ASN][1000 genomes]
rs13329278	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13329402	1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13329500	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1669870	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.96[ASN][1000 genomes]
rs1669872	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.96[ASN][1000 genomes]
rs16964891	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs16964903	1.00[GIH][hapmap]
rs16964910	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16964915	1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16964919	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16964921	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16964924	0.81[AFR][1000 genomes]
rs16964928	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16964944	1.00[GIH][hapmap]
rs16964952	1.00[GIH][hapmap]
rs1724577	1.00[GIH][hapmap]
rs1724599	0.85[GIH][hapmap]
rs1724600	0.85[GIH][hapmap]
rs1724602	0.85[GIH][hapmap]
rs2222656	0.85[GIH][hapmap]
rs2242059	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2414137	1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2414138	1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs2414145	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.96[ASN][1000 genomes]
rs2600903	1.00[GIH][hapmap]
rs2600904	1.00[GIH][hapmap]
rs28367336	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28374631	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28409636	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs28409760	0.98[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs28462026	0.82[AFR][1000 genomes]
rs28475475	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28496242	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28503750	0.99[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs28508266	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28532168	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs28556657	0.98[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs28590330	0.80[AFR][1000 genomes]
rs28633243	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28653534	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28657676	0.95[AFR][1000 genomes]
rs28669685	0.80[AFR][1000 genomes]
rs28693941	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28756182	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3764230	1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4499185	0.90[YRI][hapmap]
rs4624108	1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4774620	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap]
rs4774621	0.81[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.96[ASN][1000 genomes]
rs58029714	0.97[AFR][1000 genomes]
rs58812575	0.82[AFR][1000 genomes]
rs7163242	0.96[ASN][1000 genomes]
rs7163778	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.96[ASN][1000 genomes]
rs7164164	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7164872	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7166034	1.00[GIH][hapmap]
rs7167437	0.85[ASN][1000 genomes]
rs7167916	0.80[AFR][1000 genomes]
rs7168251	1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7169104	0.96[YRI][hapmap]
rs7169346	1.00[GIH][hapmap];0.92[YRI][hapmap]
rs7170622	0.96[YRI][hapmap]
rs7171999	0.96[ASN][1000 genomes]
rs73408415	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs73408465	0.97[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs73408469	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73408478	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73410713	0.98[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs73410715	0.82[AFR][1000 genomes]
rs7342673	0.85[GIH][hapmap]
rs744501	1.00[GIH][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs8024412	1.00[GIH][hapmap]
rs8027777	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8030307	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8035199	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8040369	1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8040558	0.81[ASW][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs8041819	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs8042235	0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs8042245	0.92[YRI][hapmap]
rs876549	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]
rs9744852	0.94[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9920739	1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[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	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52607800-52657800	Weak transcription	Small Intestine	intestine
2	chr15:52609800-52677600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:52611800-52675800	Weak transcription	Gastric	stomach
4	chr15:52613600-52666600	Weak transcription	Right Ventricle	heart
5	chr15:52620600-52659200	Weak transcription	Fetal Lung	lung
6	chr15:52621200-52666600	Weak transcription	Fetal Brain Male	brain
7	chr15:52621800-52662200	Weak transcription	Psoas Muscle	Psoas
8	chr15:52630600-52684800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:52631600-52679200	Weak transcription	Fetal Intestine Small	intestine
10	chr15:52632600-52670400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:52632800-52657400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr15:52632800-52662200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr15:52633600-52662200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:52638000-52671600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:52640200-52655000	Weak transcription	Liver	Liver
16	chr15:52640600-52666600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:52641800-52666800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:52643600-52655600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:52643800-52655400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:52644000-52664200	Weak transcription	NHLF	lung
21	chr15:52644000-52666600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr15:52644200-52661000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr15:52644200-52680800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:52644600-52654200	Weak transcription	Right Atrium	heart
25	chr15:52644600-52660200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr15:52644600-52661200	Weak transcription	Thymus	Thymus
27	chr15:52644600-52661600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:52644600-52662000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr15:52644600-52662200	Weak transcription	Fetal Muscle Leg	muscle
30	chr15:52644600-52662400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr15:52644600-52662400	Weak transcription	Fetal Stomach	stomach
32	chr15:52644600-52663800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:52644600-52663800	Weak transcription	Spleen	Spleen
34	chr15:52644600-52665400	Weak transcription	A549	lung
35	chr15:52644600-52730200	Weak transcription	Esophagus	oesophagus
36	chr15:52644800-52655600	Weak transcription	Dnd41	blood
37	chr15:52645600-52661200	Weak transcription	NH-A	brain
38	chr15:52645800-52657400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:52645800-52661000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr15:52645800-52661000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:52646000-52660400	Weak transcription	Placenta	Placenta
42	chr15:52646000-52661600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr15:52646200-52654200	Weak transcription	Brain Germinal Matrix	brain
44	chr15:52646200-52655000	Weak transcription	Fetal Thymus	thymus
45	chr15:52646200-52657200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr15:52646200-52660600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr15:52646200-52661600	Weak transcription	Left Ventricle	heart
48	chr15:52646200-52663800	Weak transcription	Lung	lung
49	chr15:52646400-52659200	Weak transcription	Colon Smooth Muscle	Colon
50	chr15:52647400-52690600	Strong transcription	Primary neutrophils fromperipheralblood	blood

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