Variant report

Variant	rs11172325
Chromosome Location	chr12:58153428-58153429
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:151)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:151 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr12:58153198-58153459	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:58152663-58153863	GM12878	blood:	n/a	n/a
3	CTCF	chr12:58153280-58153430	HMEC	breast:	n/a	n/a
4	CTCF	chr12:58153210-58153488	GM12878	blood:	n/a	n/a
5	RAD21	chr12:58153254-58153464	HepG2	liver:	n/a	n/a
6	CTCF	chr12:58153202-58153502	T-47D	breast:	n/a	n/a
7	CTCF	chr12:58153280-58153430	GM12878	blood:	n/a	n/a
8	RAD21	chr12:58153188-58153516	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr12:58153280-58153430	AG04449	skin:	n/a	n/a
10	CTCF	chr12:58153230-58153476	LNCaP	prostate:	n/a	n/a
11	CTCF	chr12:58152820-58153829	A549	lung:	n/a	n/a
12	RAD21	chr12:58153140-58153458	SK-N-SH_RA	brain:	n/a	n/a
13	CTCF	chr12:58153232-58153440	ProgFib	skin:	n/a	n/a
14	SMC3	chr12:58153223-58153518	HepG2	liver:	n/a	n/a
15	CTCF	chr12:58153340-58153490	HEK293	kidney:	n/a	n/a
16	CTCF	chr12:58153280-58153430	HEEpiC	esophagus:	n/a	n/a
17	POLR2A	chr12:58153037-58153535	HepG2	liver:	n/a	n/a
18	CTCF	chr12:58153231-58153452	A549	lung:	n/a	n/a
19	CTCF	chr12:58153280-58153430	GM12865	blood:	n/a	n/a
20	MYC	chr12:58153240-58153440	K562	blood:	n/a	n/a
21	CTCF	chr12:58153083-58153593	MCF-7	breast:	n/a	n/a
22	CTCF	chr12:58153184-58153501	IMR90	lung:	n/a	n/a
23	ZNF143	chr12:58153241-58153464	Hela-S3	cervix:	n/a	n/a
24	RAD21	chr12:58153205-58153498	HepG2	liver:	n/a	n/a
25	POLR2A	chr12:58152965-58153929	HepG2	liver:	n/a	n/a
26	USF2	chr12:58153252-58153466	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr12:58153071-58153643	MCF-7	breast:	n/a	n/a
28	CTCF	chr12:58153280-58153430	AG04450	lung:	n/a	n/a
29	CTCF	chr12:58153280-58153430	GM12875	blood:	n/a	n/a
30	RAD21	chr12:58153134-58153457	HepG2	liver:	n/a	n/a
31	SMC3	chr12:58153122-58153510	GM12878	blood:	n/a	n/a
32	CTCF	chr12:58153280-58153430	WERI-Rb-1	eye:	n/a	n/a
33	CTCF	chr12:58153235-58153430	SK-N-SH_RA	brain:	n/a	n/a
34	RAD21	chr12:58153167-58153678	MCF-7	breast:	n/a	n/a
35	CTCF	chr12:58153175-58153482	K562	blood:	n/a	n/a
36	CTCF	chr12:58153246-58153443	GM10266	blood:	n/a	n/a
37	CTCF	chr12:58153162-58153528	A549	lung:	n/a	n/a
38	CTCF	chr12:58153280-58153430	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr12:58153280-58153430	HRPEpiC	eye:	n/a	n/a
40	CTCF	chr12:58153280-58153430	NHEK	skin:	n/a	n/a
41	CTCF	chr12:58153280-58153430	BE2_C	brain:	n/a	n/a
42	ZNF143	chr12:58153187-58153501	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr12:58153237-58153476	GM13977	blood:	n/a	n/a
44	CTCF	chr12:58153233-58153468	HUVEC	blood vessel:	n/a	n/a
45	RAD21	chr12:58153206-58153588	ECC-1	luminal epithelium:	n/a	n/a
46	CTCF	chr12:58153280-58153430	GM12873	blood:	n/a	n/a
47	CTCF	chr12:58153320-58153470	HCT-116	colon:	n/a	n/a
48	CTCF	chr12:58153238-58153435	HepG2	liver:	n/a	n/a
49	CTCF	chr12:58153300-58153450	AG10803	skin:	n/a	n/a
50	CTCF	chr12:58153217-58153483	MCF-7	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:57910612..57912523-chr12:58153055..58155888,2	K562	blood:
2	chr12:58152878..58153571-chr12:58299170..58299699,2	MCF-7	breast:
3	chr12:58109491..58111128-chr12:58152732..58154720,2	K562	blood:
4	chr12:57910530..57914371-chr12:58151795..58155888,4	K562	blood:

No data

Variant related genes	Relation type
CDK4	TF binding region
ENSG00000135506	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000208028	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11172322	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11172327	0.83[LWK][hapmap];1.00[MEX][hapmap]
rs11172336	0.83[YRI][hapmap]
rs11829917	0.87[ASW][hapmap];0.91[YRI][hapmap]
rs17119958	1.00[MEX][hapmap]
rs3473	0.83[YRI][hapmap]
rs8176348	0.87[ASW][hapmap];1.00[MEX][hapmap]
rs8176353	0.88[LWK][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap]

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	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS 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 miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv899123	chr12:58118248-58155023	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv826384	chr12:58124758-58157850	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
9	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11172325	MEST	trans	lymphoblastoid	seeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58150200-58154400	Weak transcription	Psoas Muscle	Psoas
2	chr12:58150400-58158400	Weak transcription	Right Atrium	heart
3	chr12:58150600-58153600	Weak transcription	Fetal Kidney	kidney
4	chr12:58150600-58156400	Weak transcription	Small Intestine	intestine
5	chr12:58150600-58156400	Weak transcription	Hela-S3	cervix
6	chr12:58150600-58158600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:58150800-58154600	Strong transcription	Fetal Stomach	stomach
8	chr12:58150800-58156200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:58150800-58156800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:58151000-58153800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:58151000-58154000	Strong transcription	Dnd41	blood
12	chr12:58151000-58154600	Weak transcription	Fetal Brain Male	brain
13	chr12:58151000-58154800	Weak transcription	HepG2	liver
14	chr12:58151000-58155400	Strong transcription	Brain Germinal Matrix	brain
15	chr12:58151000-58156000	Strong transcription	Fetal Intestine Small	intestine
16	chr12:58151000-58156600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr12:58151200-58154000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:58151400-58153600	Strong transcription	Fetal Intestine Large	intestine
19	chr12:58151600-58154000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:58151600-58154000	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:58151600-58154000	Strong transcription	Thymus	Thymus
22	chr12:58151600-58154200	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:58151600-58154200	Strong transcription	Stomach Smooth Muscle	stomach
24	chr12:58151600-58155000	Strong transcription	Primary B cells from cord blood	blood
25	chr12:58151600-58155200	Strong transcription	Primary T cells from cord blood	blood
26	chr12:58151600-58155800	Strong transcription	Fetal Brain Female	brain
27	chr12:58151600-58156400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:58151800-58156200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:58152200-58156600	Weak transcription	Fetal Lung	lung
30	chr12:58152200-58160000	Weak transcription	K562	blood
31	chr12:58152400-58154200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr12:58152400-58154400	Weak transcription	HMEC	breast
33	chr12:58152400-58154800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:58152400-58156400	Strong transcription	NHEK	skin
35	chr12:58152400-58157400	Weak transcription	HSMMtube	muscle
36	chr12:58152600-58156400	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr12:58152600-58156800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:58152600-58157200	Weak transcription	Liver	Liver
39	chr12:58152800-58153800	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr12:58152800-58154000	Weak transcription	Colonic Mucosa	Colon
41	chr12:58152800-58155200	Weak transcription	Colon Smooth Muscle	Colon
42	chr12:58152800-58156400	Weak transcription	Brain Substantia Nigra	brain
43	chr12:58152800-58158000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:58153000-58153600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr12:58153000-58153800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:58153000-58154000	Genic enhancers	Primary B cells from peripheral blood	blood
47	chr12:58153000-58154000	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr12:58153000-58154000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:58153000-58155000	Weak transcription	Right Ventricle	heart
50	chr12:58153000-58155400	Weak transcription	Ovary	ovary

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