Variant report

Variant	rs11842169
Chromosome Location	chr13:53424850-53424851
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	POLR2A	chr13:53424788-53425506	H1-hESC	embryonic stem cell:	n/a	n/a
2	KAP1	chr13:53424626-53425277	U2OS	brain:	n/a	n/a
3	GABPA	chr13:53424748-53425123	A549	lung:	n/a	n/a
4	REST	chr13:53424424-53426110	HL-60	blood:	n/a	chr13:53424988-53425001 chr13:53425721-53425731 chr13:53425716-53425729 chr13:53425719-53425733 chr13:53424936-53424945
5	HA-E2F1	chr13:53424727-53426076	MCF-7	breast:	n/a	chr13:53425443-53425453 chr13:53425348-53425360
6	JUN	chr13:53424644-53425270	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr13:53424823-53425214	MCF-7	breast:	n/a	chr13:53425183-53425192
8	MXI1	chr13:53424608-53425505	IMR90	lung:	n/a	n/a
9	GABPA	chr13:53424675-53425230	H1-hESC	embryonic stem cell:	n/a	n/a
10	REST	chr13:53424828-53425017	PANC-1	pancreas:	n/a	chr13:53424988-53425001 chr13:53424936-53424945
11	TEAD4	chr13:53424379-53424865	H1-hESC	embryonic stem cell:	n/a	n/a
12	GABPA	chr13:53424813-53425148	GM12878	blood:	n/a	n/a
13	MAX	chr13:53424846-53426127	SK-N-SH	brain:	n/a	chr13:53425183-53425192 chr13:53425990-53425999 chr13:53425349-53425359 chr13:53425990-53425999
14	CTCF	chr13:53424760-53424910	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr13:53424812-53425516	GM12878	blood:	n/a	n/a
16	MAZ	chr13:53424845-53425146	GM12878	blood:	n/a	n/a
17	E2F4	chr13:53424776-53425168	MCF10A-Er-Src	breast:	n/a	n/a
18	GABPA	chr13:53424514-53425804	MCF-7	breast:	n/a	n/a
19	REST	chr13:53424450-53425491	MCF-7	breast:	n/a	chr13:53424988-53425001 chr13:53424936-53424945
20	RAD21	chr13:53424349-53425271	H1-hESC	embryonic stem cell:	n/a	chr13:53425131-53425141 chr13:53424651-53424670 chr13:53425129-53425141
21	TEAD4	chr13:53424572-53425255	A549	lung:	n/a	n/a
22	ZNF143	chr13:53423976-53425385	H1-hESC	embryonic stem cell:	n/a	chr13:53425004-53425014 chr13:53425128-53425138 chr13:53424048-53424058
23	REST	chr13:53424516-53425402	SK-N-SH	brain:	n/a	chr13:53424988-53425001 chr13:53424936-53424945
24	CTCF	chr13:53424700-53424850	AG09309	skin:	n/a	n/a
25	CREB1	chr13:53424679-53425212	HepG2	liver:	n/a	n/a
26	RCOR1	chr13:53424761-53425124	HepG2	liver:	n/a	n/a
27	EGR1	chr13:53424430-53425182	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTBP2	chr13:53423916-53425961	H1-hESC	embryonic stem cell:	n/a	n/a
29	CEBPB	chr13:53424622-53425041	H1-hESC	embryonic stem cell:	n/a	n/a
30	MYC	chr13:53424828-53425214	MCF-7	breast:	n/a	chr13:53425183-53425192
31	SIN3AK20	chr13:53424429-53425195	H1-hESC	embryonic stem cell:	n/a	n/a
32	ELF1	chr13:53424672-53425494	SK-N-SH	brain:	n/a	chr13:53424939-53424951 chr13:53425439-53425448 chr13:53425443-53425455
33	CREB1	chr13:53424417-53425185	H1-hESC	embryonic stem cell:	n/a	n/a
34	REST	chr13:53424580-53425240	U87	brain:	n/a	chr13:53424988-53425001 chr13:53424936-53424945
35	STAT5A	chr13:53424776-53425414	GM12878	blood:	n/a	chr13:53424788-53424799
36	PML	chr13:53424747-53426299	GM12878	blood:	n/a	n/a
37	RUNX3	chr13:53424797-53426168	GM12878	blood:	n/a	n/a
38	TCF12	chr13:53424762-53425268	ECC-1	luminal epithelium:	n/a	n/a
39	ELF1	chr13:53424718-53425288	MCF-7	breast:	n/a	chr13:53424939-53424951
40	SIN3A	chr13:53423625-53426612	H1-hESC	embryonic stem cell:	n/a	chr13:53424048-53424057 chr13:53425722-53425731 chr13:53424040-53424053 chr13:53424469-53424478 chr13:53424988-53424997 chr13:53425401-53425414
41	MAX	chr13:53424735-53425748	ECC-1	luminal epithelium:	n/a	chr13:53425183-53425192 chr13:53425349-53425359
42	POLR2A	chr13:53423515-53426172	H1-neurons	neurons:	n/a	n/a
43	REST	chr13:53424440-53425277	U87	brain:	n/a	chr13:53424988-53425001 chr13:53424936-53424945
44	TAF7	chr13:53424696-53425180	H1-hESC	embryonic stem cell:	n/a	n/a
45	REST	chr13:53422663-53426246	HL-60	blood:	n/a	chr13:53424040-53424053 chr13:53422864-53422877 chr13:53424988-53425001 chr13:53425721-53425731 chr13:53424411-53424421 chr13:53425716-53425729 chr13:53422984-53422998 chr13:53422986-53422996 chr13:53425719-53425733 chr13:53424936-53424945 chr13:53424047-53424057
46	RAD21	chr13:53424460-53425134	H1-hESC	embryonic stem cell:	n/a	chr13:53424651-53424670
47	FOXP2	chr13:53424760-53425060	SK-N-MC	brain:	n/a	n/a
48	GABPA	chr13:53424695-53425604	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr13:53424784-53425220	SK-N-SH	brain:	n/a	n/a
50	CREB1	chr13:53424679-53426115	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:53424812-53424862	BJ	skin:	n/a
2	chr13:53424812-53424862	HCPEpiC	choroid plexus:	n/a
3	chr13:53424812-53424862	AG09309	skin:	n/a
4	chr13:53424812-53424862	HL-60	blood:	n/a
5	chr13:53424812-53424862	ovcar-3	ovarian:	n/a
6	chr13:53424812-53424862	NHBE	bronchial:	n/a
7	chr13:53424812-53424862	IMR90	lung:	fetal
8	chr13:53424812-53424862	HepG2	liver:	n/a
9	chr13:53424812-53424862	AG09319	gingival:	n/a
10	chr13:53424812-53424862	GM12892	blood:	n/a
11	chr13:53424812-53424862	CMK	blood:	n/a
12	chr13:53424812-53424862	LNCaP	prostate:	n/a
13	chr13:53424812-53424862	Caco-2	colon:	n/a
14	chr13:53424812-53424862	HMEC	breast:	n/a
15	chr13:53424812-53424862	ECC-1	luminal epithelium:	n/a
16	chr13:53424812-53424862	ProgFib	skin:	n/a
17	chr13:53424812-53424862	SK-N-MC	brain:	n/a
18	chr13:53424812-53424862	HNPCEpiC	eye:	n/a
19	chr13:53424812-53424862	A549	lung:	n/a
20	chr13:53424812-53424862	Hepatocyte	liver:	n/a
21	chr13:53424812-53424862	GM06990	blood:	n/a
22	chr13:53424812-53424862	AG04449	skin:	fetal
23	chr13:53424812-53424862	GM19239	blood:	n/a
24	chr13:53424812-53424862	T-47D	breast:	n/a
25	chr13:53424812-53424862	NH-A	brain:	n/a
26	chr13:53424812-53424862	HCF	heart:	n/a
27	chr13:53424812-53424862	Hela-S3	cervix:	n/a
28	chr13:53424812-53424862	HCM	heart:	n/a
29	chr13:53424812-53424862	RPTEC	kidney:	n/a
30	chr13:53424812-53424862	PrEC	prostate:	n/a
31	chr13:53424812-53424862	HIPEpiC	eye:	n/a
32	chr13:53424812-53424862	U87	brain:	n/a
33	chr13:53424812-53424862	NT2-D1	testis:	n/a
34	chr13:53424812-53424862	HRCEpiC	kidney:	n/a
35	chr13:53424812-53424862	SKMC	muscle:	n/a
36	chr13:53424812-53424862	AoSMC	blood vessel:	n/a
37	chr13:53424812-53424862	HEEpiC	esophagus:	n/a
38	chr13:53424812-53424862	HEK293	kidney:	embryo
39	chr13:53424812-53424862	HUVEC	blood vessel:	n/a
40	chr13:53424812-53424862	AG10803	skin:	n/a
41	chr13:53424812-53424862	HRPEpiC	eye:	n/a
42	chr13:53424812-53424862	AG04450	lung:	fetal
43	chr13:53424812-53424862	NHDF-neo	bronchial:	n/a
44	chr13:53424812-53424862	HRE	kidney:	n/a
45	chr13:53424812-53424862	NB4	blood:	n/a
46	chr13:53424812-53424862	HPAEpiC	pulmonary alveolar:	n/a
47	chr13:53424812-53424862	GM12891	blood:	n/a
48	chr13:53424812-53424862	GM12878	blood:	n/a
49	chr13:53424812-53424862	SK-N-SH_RA	brain:	n/a
50	chr13:53424812-53424862	MCF10A-Er-Src	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:53424499..53425128-chr13:53541822..53542463,2	MCF-7	breast:
2	chr13:53423777..53426647-chr13:53440227..53445526,5	MCF-7	breast:
3	chr13:53416128..53422445-chr13:53423052..53427915,11	MCF-7	breast:
4	chr13:53424748..53427468-chr13:53541401..53543631,2	MCF-7	breast:
5	chr13:53225548..53228779-chr13:53423444..53428429,4	MCF-7	breast:
6	chr13:53423819..53426475-chr13:53542000..53544855,3	MCF-7	breast:
7	chr13:53226333..53229941-chr13:53424392..53427948,4	MCF-7	breast:
8	chr13:53385344..53387771-chr13:53424492..53426608,2	MCF-7	breast:
9	chr13:53423269..53426675-chr13:53427472..53433524,8	MCF-7	breast:
10	chr13:53413901..53415786-chr13:53423425..53426036,2	MCF-7	breast:
11	chr13:53189284..53191816-chr13:53423878..53426423,2	MCF-7	breast:
12	chr13:53424477..53427390-chr13:53433560..53435155,3	MCF-7	breast:
13	chr13:53419410..53422161-chr13:53423908..53427048,5	MCF-7	breast:
14	chr13:53424598..53426748-chr13:53456688..53458919,2	MCF-7	breast:

Variant related genes	Relation type
PCDH8	TF binding region
PCDH8	CpG island
ENSG00000139675	Chromatin interaction
ENSG00000165416	Chromatin interaction
ENSG00000250299	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11840632	1.00[AMR][1000 genomes]
rs564456	1.00[AMR][1000 genomes]
rs57622965	1.00[AMR][1000 genomes]
rs58221735	1.00[AMR][1000 genomes]
rs59233409	1.00[AMR][1000 genomes]
rs73494246	1.00[AMR][1000 genomes]
rs73494253	1.00[AMR][1000 genomes]
rs73494254	1.00[AMR][1000 genomes]
rs73494260	1.00[AMR][1000 genomes]
rs73494285	1.00[AMR][1000 genomes]
rs73494292	1.00[AMR][1000 genomes]
rs73494295	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv900089	chr13:53385334-53429453	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv1810064	chr13:53412849-53441018	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1822518	chr13:53412849-53441018	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
6	esv1829072	chr13:53412849-53441018	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv523092	chr13:53419139-53429453	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv455889	chr13:53419139-53466127	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv561661	chr13:53419139-53466127	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53421800-53426200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
2	chr13:53423000-53425000	Flanking Active TSS	Fetal Brain Female	brain
3	chr13:53423600-53426000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
4	chr13:53423800-53425000	ZNF genes & repeats	Spleen	Spleen
5	chr13:53423800-53426000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
6	chr13:53423800-53426800	Enhancers	Fetal Brain Male	brain
7	chr13:53424200-53425400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
8	chr13:53424200-53425800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:53424200-53426000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr13:53424200-53426000	Active TSS	Brain Substantia Nigra	brain
11	chr13:53424400-53425000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
12	chr13:53424400-53425000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
13	chr13:53424400-53425000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
14	chr13:53424400-53425600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
15	chr13:53424400-53426200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr13:53424400-53426400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr13:53424400-53426800	Flanking Active TSS	GM12878-XiMat	blood
18	chr13:53424600-53425000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr13:53424600-53425000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr13:53424600-53425000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr13:53424600-53425000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr13:53424600-53425000	Flanking Active TSS	Colon Smooth Muscle	Colon
23	chr13:53424600-53425000	Bivalent Enhancer	Placenta	Placenta
24	chr13:53424600-53425000	Bivalent Enhancer	Fetal Thymus	thymus
25	chr13:53424600-53425000	Bivalent Enhancer	Stomach Mucosa	stomach
26	chr13:53424600-53425200	Active TSS	Primary B cells from cord blood	blood
27	chr13:53424600-53425200	Bivalent/Poised TSS	Colonic Mucosa	Colon
28	chr13:53424600-53425200	Active TSS	Duodenum Mucosa	Duodenum
29	chr13:53424600-53425200	Flanking Bivalent TSS/Enh	Lung	lung
30	chr13:53424600-53425200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
31	chr13:53424600-53425200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
32	chr13:53424600-53425400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
33	chr13:53424600-53425600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr13:53424600-53425600	Flanking Active TSS	Right Ventricle	heart
35	chr13:53424600-53425800	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr13:53424600-53425800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
37	chr13:53424600-53426000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr13:53424600-53426000	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr13:53424600-53426000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
40	chr13:53424600-53426000	Bivalent/Poised TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr13:53424600-53426000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
42	chr13:53424600-53426000	Active TSS	Brain Angular Gyrus	brain
43	chr13:53424600-53426200	Active TSS	H1 Cell Line	embryonic stem cell
44	chr13:53424600-53426200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr13:53424600-53426200	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr13:53424600-53426200	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr13:53424600-53426200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr13:53424600-53426200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr13:53424600-53426200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
50	chr13:53424600-53426200	Active TSS	Pancreatic Islets	Pancreatic Islet

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