Variant report

Variant	rs16964639
Chromosome Location	chr15:52239463-52239464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:52239074-52239472	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr15:52239146-52239525	HepG2	liver:	n/a	n/a
3	GATA3	chr15:52239321-52239804	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr15:52239254-52239693	SK-N-SH	brain:	n/a	chr15:52239317-52239324

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:52238261..52241204-chr15:52243330..52245853,2	MCF-7	breast:
2	chr15:52232743..52235085-chr15:52238669..52241010,2	MCF-7	breast:
3	chr15:52230609..52232827-chr15:52238038..52240030,2	MCF-7	breast:
4	chr15:52237326..52240227-chr15:52247479..52249462,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAPK6-3	chr15:52239187-52239491	NONHSAT043889
2	lnc-MAPK6-3	chr15:52239187-52239492	NONHSAT043892
3	lnc-MAPK6-3	chr15:52239187-52239492	NONHSAT043888
4	lnc-MAPK6-3	chr15:52239187-52239464	NONHSAT043894

No data

Variant related genes	Relation type
MAPK6	TF binding region
ENSG00000069956	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs16953082	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964505	0.83[EUR][1000 genomes]
rs16964506	0.83[EUR][1000 genomes]
rs16964507	0.83[EUR][1000 genomes]
rs16964508	0.83[EUR][1000 genomes]
rs16964510	0.83[EUR][1000 genomes]
rs16964518	0.83[EUR][1000 genomes]
rs16964528	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs16964532	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964555	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964561	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964579	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964585	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964596	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964645	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991267	0.90[ASN][1000 genomes]
rs2258248	0.90[ASN][1000 genomes]
rs2570265	0.90[ASN][1000 genomes]
rs2593181	0.90[ASN][1000 genomes]
rs2593184	0.90[ASN][1000 genomes]
rs2623291	0.90[ASN][1000 genomes]
rs2959296	0.90[ASN][1000 genomes]
rs56221158	0.80[EUR][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	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1053788	chr15:52223389-52307138	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	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	chr15:52179600-52259800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:52200400-52262200	Weak transcription	Stomach Mucosa	stomach
3	chr15:52212400-52241600	Weak transcription	Small Intestine	intestine
4	chr15:52218000-52243200	Weak transcription	Fetal Heart	heart
5	chr15:52222600-52259800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr15:52223200-52245400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:52226000-52255200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:52226200-52242600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:52226200-52254800	Strong transcription	Thymus	Thymus
10	chr15:52226200-52255000	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr15:52226200-52259400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:52227400-52255000	Strong transcription	Liver	Liver
13	chr15:52227400-52258400	Strong transcription	Dnd41	blood
14	chr15:52227800-52255000	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr15:52229400-52249000	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:52229800-52254200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:52232800-52256000	Strong transcription	Fetal Muscle Leg	muscle
18	chr15:52233000-52258000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr15:52233200-52250800	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:52233200-52255200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr15:52233200-52255200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:52233400-52248000	Strong transcription	Primary T cells from cord blood	blood
23	chr15:52233600-52258000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr15:52234400-52240800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:52234600-52242200	Weak transcription	Psoas Muscle	Psoas
26	chr15:52235600-52255000	Strong transcription	Duodenum Mucosa	Duodenum
27	chr15:52235600-52255200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:52235600-52256000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr15:52235600-52258000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:52235800-52255000	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr15:52235800-52255000	Strong transcription	A549	lung
32	chr15:52235800-52255000	Strong transcription	Osteobl	bone
33	chr15:52235800-52255200	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr15:52235800-52255200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:52235800-52256000	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:52235800-52258000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:52235800-52258600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr15:52235800-52259200	Strong transcription	Hela-S3	cervix
39	chr15:52236000-52248400	Strong transcription	GM12878-XiMat	blood
40	chr15:52236000-52248600	Strong transcription	HSMMtube	muscle
41	chr15:52236000-52255000	Strong transcription	Stomach Smooth Muscle	stomach
42	chr15:52236000-52255200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:52236000-52255200	Strong transcription	Fetal Lung	lung
44	chr15:52236000-52255600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr15:52236000-52256200	Strong transcription	HepG2	liver
46	chr15:52236000-52258000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:52236000-52258600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr15:52236000-52258800	Strong transcription	Fetal Thymus	thymus
49	chr15:52236200-52255600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr15:52236200-52258800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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