Variant report

Variant	rs60893904
Chromosome Location	chr15:50641807-50641808
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr15:50641598-50641846	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr15:50641221-50643664	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr15:50641547-50641904	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr15:50641549-50641891	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr15:50641590-50641881	MCF10A-Er-Src	breast:	n/a	n/a
6	ARID3A	chr15:50641786-50641922	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50474061..50475974-chr15:50641012..50643370,2	MCF-7	breast:
2	chr15:50641443..50644268-chr15:50716209..50717916,2	MCF-7	breast:
3	chr15:50487139..50490001-chr15:50641333..50643043,2	K562	blood:
4	chr15:50625762..50628715-chr15:50641413..50643751,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HDC-2	chr15:50641135-50647076	NONHSAT042404

No data

Variant related genes	Relation type
ENSG00000271819	TF binding region
ENSG00000140284	Chromatin interaction
ENSG00000104043	Chromatin interaction
ENSG00000138592	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10083714	0.82[ASN][1000 genomes]
rs10152574	0.92[ASN][1000 genomes]
rs11491094	0.82[ASN][1000 genomes]
rs16963562	0.93[AFR][1000 genomes]
rs16963571	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16963573	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16963578	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16963582	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16963638	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1896169	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1955101	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs55697237	0.92[ASN][1000 genomes]
rs55774471	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55950921	0.92[ASN][1000 genomes]
rs56812974	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58903525	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59847008	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs717025	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7177488	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74012326	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74012336	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74012366	0.92[ASN][1000 genomes]
rs74012367	0.92[ASN][1000 genomes]
rs8028745	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8029259	0.82[ASN][1000 genomes]
rs8029439	0.82[ASN][1000 genomes]
rs8034492	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8040420	0.86[ASN][1000 genomes]
rs8040483	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs953159	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9652452	0.82[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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50600800-50643000	Weak transcription	Fetal Thymus	thymus
2	chr15:50600800-50643400	Weak transcription	Fetal Muscle Leg	muscle
3	chr15:50600800-50644200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:50600800-50644600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:50601400-50642800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:50608800-50642800	Weak transcription	Hela-S3	cervix
7	chr15:50615200-50644000	Weak transcription	HSMMtube	muscle
8	chr15:50618200-50642400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:50618400-50646000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:50621200-50646000	Weak transcription	Gastric	stomach
11	chr15:50622000-50642400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr15:50623400-50643000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:50623800-50644200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:50623800-50645600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr15:50624000-50644000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:50624000-50644000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:50624000-50644000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:50627600-50642400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:50627600-50643000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr15:50627800-50643600	Weak transcription	Lung	lung
21	chr15:50628400-50643600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr15:50629000-50642800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr15:50630000-50643600	Weak transcription	Placenta	Placenta
24	chr15:50631000-50643400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:50631400-50643400	Weak transcription	Fetal Stomach	stomach
26	chr15:50631400-50643800	Weak transcription	Fetal Intestine Small	intestine
27	chr15:50631600-50642400	Weak transcription	Thymus	Thymus
28	chr15:50633800-50645600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:50634400-50642200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr15:50634400-50642200	Weak transcription	Small Intestine	intestine
31	chr15:50635800-50643600	Weak transcription	Psoas Muscle	Psoas
32	chr15:50636400-50642400	Weak transcription	Fetal Lung	lung
33	chr15:50636800-50642200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr15:50638600-50642800	Weak transcription	Stomach Mucosa	stomach
35	chr15:50638800-50644000	Weak transcription	HMEC	breast
36	chr15:50638800-50644600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:50639000-50642600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:50639200-50642200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr15:50639200-50644000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:50639400-50642200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr15:50639400-50643400	Weak transcription	Left Ventricle	heart
42	chr15:50639600-50642200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr15:50639800-50642400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr15:50639800-50643000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr15:50640000-50642800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:50640600-50644000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr15:50640800-50642000	Enhancers	Primary B cells from cord blood	blood
48	chr15:50640800-50642000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr15:50640800-50642200	Enhancers	Fetal Brain Male	brain
50	chr15:50640800-50642400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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