Variant report

Variant	rs13162858
Chromosome Location	chr5:179920933-179920934
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr5:179920925-179922244	GM12878	blood:	n/a	chr5:179921385-179921397 chr5:179921995-179922007 chr5:179921997-179922006 chr5:179921350-179921359 chr5:179921994-179922003 chr5:179922000-179922009
2	POLR2A	chr5:179920928-179921934	MCF-7	breast:	n/a	n/a
3	SP1	chr5:179920907-179921840	HCT-116	colon:	n/a	chr5:179921320-179921341 chr5:179921245-179921257 chr5:179921246-179921255 chr5:179921247-179921256 chr5:179921245-179921257 chr5:179921246-179921256 chr5:179921247-179921256 chr5:179921245-179921256 chr5:179921242-179921256 chr5:179921246-179921256
4	MYBL2	chr5:179920928-179921477	HepG2	liver:	n/a	n/a
5	SIN3AK20	chr5:179920903-179922557	MCF-7	breast:	n/a	n/a
6	SIX5	chr5:179920866-179921605	A549	lung:	n/a	n/a
7	MAX	chr5:179920919-179922500	A549	lung:	n/a	n/a
8	SP1	chr5:179920852-179921650	A549	lung:	n/a	chr5:179921320-179921341 chr5:179921245-179921257 chr5:179921246-179921255 chr5:179921247-179921256 chr5:179921245-179921257 chr5:179921246-179921256 chr5:179921247-179921256 chr5:179921245-179921256 chr5:179921242-179921256 chr5:179921246-179921256
9	POLR2A	chr5:179920875-179922241	PANC-1	pancreas:	n/a	n/a
10	JUND	chr5:179920886-179922338	GM12878	blood:	n/a	n/a
11	POLR2A	chr5:179920929-179922160	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr5:179920686-179921907	HepG2	liver:	n/a	n/a
13	HEY1	chr5:179920863-179921973	HepG2	liver:	n/a	chr5:179921203-179921218
14	JUND	chr5:179920916-179922384	SK-N-SH	brain:	n/a	n/a
15	REST	chr5:179920877-179922228	H1-neurons	neurons:	n/a	chr5:179922163-179922183 chr5:179921255-179921268 chr5:179922051-179922064
16	POLR2A	chr5:179920850-179922690	SK-N-MC	brain:	n/a	n/a
17	MAX	chr5:179920922-179921727	HCT-116	colon:	n/a	n/a
18	POLR2A	chr5:179920892-179921776	GM12891	blood:	n/a	n/a
19	POLR2A	chr5:179920888-179922215	MCF-7	breast:	n/a	n/a
20	NR2F2	chr5:179920863-179921350	K562	blood:	n/a	n/a
21	RUNX3	chr5:179920924-179921497	GM12878	blood:	n/a	n/a
22	EP300	chr5:179920903-179921773	ECC-1	luminal epithelium:	n/a	chr5:179921385-179921394 chr5:179921350-179921359 chr5:179921387-179921396
23	MAX	chr5:179920933-179921693	A549	lung:	n/a	n/a
24	POLR2A	chr5:179920904-179921558	SK-N-MC	brain:	n/a	n/a
25	BCL3	chr5:179920888-179921352	A549	lung:	n/a	n/a
26	SP1	chr5:179920855-179921632	A549	lung:	n/a	chr5:179921320-179921341 chr5:179921245-179921257 chr5:179921246-179921255 chr5:179921247-179921256 chr5:179921245-179921257 chr5:179921246-179921256 chr5:179921247-179921256 chr5:179921245-179921256 chr5:179921242-179921256 chr5:179921246-179921256
27	TCF12	chr5:179920762-179921882	A549	lung:	n/a	n/a
28	E2F6	chr5:179920931-179921558	H1-hESC	embryonic stem cell:	n/a	chr5:179921246-179921255 chr5:179921250-179921260
29	POLR2A	chr5:179920931-179921722	HL-60	blood:	n/a	n/a
30	EP300	chr5:179920917-179921474	A549	lung:	n/a	chr5:179921385-179921394 chr5:179921350-179921359 chr5:179921387-179921396
31	POLR2A	chr5:179920906-179922025	HUVEC	blood vessel:	n/a	n/a
32	TAF1	chr5:179920897-179921560	A549	lung:	n/a	n/a
33	BCLAF1	chr5:179920923-179921525	GM12878	blood:	n/a	chr5:179921385-179921398
34	MTA3	chr5:179920906-179921349	GM12878	blood:	n/a	n/a
35	TAF1	chr5:179920919-179922229	H1-hESC	embryonic stem cell:	n/a	n/a
36	GATA3	chr5:179920927-179921555	A549	lung:	n/a	n/a
37	POLR2A	chr5:179920863-179921400	GM12892	blood:	n/a	n/a
38	SREBP1	chr5:179920909-179921709	GM12878	blood:	n/a	n/a
39	POLR2A	chr5:179920882-179921601	PFSK-1	brain:	n/a	n/a
40	TEAD4	chr5:179920917-179921479	K562	blood:	n/a	n/a
41	REST	chr5:179920933-179921331	A549	lung:	n/a	chr5:179921255-179921268
42	POLR2A	chr5:179920852-179921643	PANC-1	pancreas:	n/a	n/a
43	PML	chr5:179920880-179921622	GM12878	blood:	n/a	n/a
44	HCFC1	chr5:179920921-179922441	Hela-S3	cervix:	n/a	n/a
45	MAZ	chr5:179920927-179922286	IMR90	lung:	n/a	n/a
46	TAF1	chr5:179920913-179921734	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr5:179920916-179922606	K562	blood:	n/a	n/a
48	POLR2A	chr5:179920742-179921634	U87	brain:	n/a	n/a
49	MXI1	chr5:179920913-179922845	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr5:179920851-179922071	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:179920260..179922999-chr5:180038598..180040134,2	MCF-7	breast:
2	chr5:179720972..179723069-chr5:179918796..179921248,2	MCF-7	breast:
3	chr5:179920138..179923580-chr5:179954774..179958751,3	MCF-7	breast:
4	chr5:179778332..179781251-chr5:179920436..179923318,3	MCF-7	breast:
5	chr5:179919075..179921338-chr5:180210769..180213087,2	MCF-7	breast:
6	chr5:179718755..179721306-chr5:179919977..179922949,4	MCF-7	breast:

Variant related genes	Relation type
CNOT6	TF binding region
ENSG00000113300	Chromatin interaction
ENSG00000248367	Chromatin interaction
ENSG00000050748	Chromatin interaction
ENSG00000131459	Chromatin interaction
ENSG00000037280	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs13158465	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62405496	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
4	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
6	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
7	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
8	nsv1023537	chr5:179791679-179982822	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv537985	chr5:179791679-179982822	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1019519	chr5:179866730-179959408	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv830564	chr5:179867394-180010096	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	esv3356496	chr5:179920371-179922919	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179915000-179921000	Weak transcription	Aorta	Aorta
2	chr5:179918400-179921000	Weak transcription	Lung	lung
3	chr5:179918600-179921000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:179918600-179921000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:179918800-179921600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:179919000-179921000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:179919000-179921000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:179919800-179921400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:179920000-179921200	Enhancers	Fetal Brain Male	brain
10	chr5:179920200-179921000	Enhancers	Primary B cells from cord blood	blood
11	chr5:179920200-179921000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:179920200-179921000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:179920200-179921000	Enhancers	Pancreas	Pancrea
14	chr5:179920200-179922200	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr5:179920400-179921000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:179920400-179921000	Enhancers	Primary hematopoietic stem cells	blood
17	chr5:179920400-179921000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:179920400-179921000	Enhancers	Stomach Mucosa	stomach
19	chr5:179920400-179921200	Enhancers	Fetal Heart	heart
20	chr5:179920400-179921600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr5:179920400-179922200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:179920400-179922200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:179920400-179922200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:179920400-179922200	Active TSS	Brain Substantia Nigra	brain
25	chr5:179920400-179922200	Active TSS	Duodenum Mucosa	Duodenum
26	chr5:179920400-179922200	Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr5:179920400-179922200	Active TSS	Stomach Smooth Muscle	stomach
28	chr5:179920400-179922400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:179920400-179922400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr5:179920400-179922800	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr5:179920400-179923000	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr5:179920400-179923200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:179920400-179923400	Active TSS	GM12878-XiMat	blood
34	chr5:179920600-179921000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr5:179920600-179921000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr5:179920600-179921000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:179920600-179921000	Enhancers	Fetal Intestine Large	intestine
38	chr5:179920600-179921000	Enhancers	Placenta Amnion	Placenta Amnion
39	chr5:179920600-179921000	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr5:179920600-179921200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr5:179920600-179921600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr5:179920600-179921800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:179920600-179922000	Active TSS	Colonic Mucosa	Colon
44	chr5:179920600-179922200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:179920600-179922200	Active TSS	Primary T cells from cord blood	blood
46	chr5:179920600-179922200	Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr5:179920600-179922200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:179920600-179922200	Active TSS	Brain Cingulate Gyrus	brain
49	chr5:179920600-179922200	Active TSS	Fetal Brain Female	brain
50	chr5:179920600-179922200	Active TSS	Rectal Mucosa Donor 31	rectum

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