Variant report

Variant	rs12424638
Chromosome Location	chr12:49318800-49318801
allele	A/G
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	USF1	chr12:49318580-49318939	SK-N-SH	brain:	n/a	n/a
2	MAX	chr12:49318443-49319168	H1-hESC	embryonic stem cell:	n/a	chr12:49318695-49318702 chr12:49318745-49318754 chr12:49318693-49318704 chr12:49318693-49318703 chr12:49318694-49318703 chr12:49318690-49318705 chr12:49318693-49318704 chr12:49318743-49318756 chr12:49318694-49318703 chr12:49318744-49318755 chr12:49318692-49318705 chr12:49318694-49318704
3	ELF1	chr12:49318291-49319474	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:49318295-49319719	GM12892	blood:	n/a	n/a
5	POLR2A	chr12:49318179-49319816	GM12892	blood:	n/a	n/a
6	RELA	chr12:49318165-49319537	GM19193	blood:	n/a	chr12:49318256-49318265 chr12:49318256-49318265
7	ZBTB7A	chr12:49318276-49319617	ECC-1	luminal epithelium:	n/a	n/a
8	TAF1	chr12:49318407-49319544	H1-hESC	embryonic stem cell:	n/a	n/a
9	CREB1	chr12:49318336-49318877	A549	lung:	n/a	n/a
10	USF2	chr12:49318333-49318868	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:49318294-49319845	MCF-7	breast:	n/a	n/a
12	ATF2	chr12:49318198-49318892	GM12878	blood:	n/a	chr12:49318762-49318776
13	MAX	chr12:49318314-49319133	ECC-1	luminal epithelium:	n/a	chr12:49318695-49318702 chr12:49318745-49318754 chr12:49318693-49318704 chr12:49318693-49318703 chr12:49318694-49318703 chr12:49318690-49318705 chr12:49318693-49318704 chr12:49318743-49318756 chr12:49318694-49318703 chr12:49318744-49318755 chr12:49318692-49318705 chr12:49318694-49318704
14	POLR2A	chr12:49318723-49319592	PFSK-1	brain:	n/a	n/a
15	MAX	chr12:49318264-49319714	A549	lung:	n/a	chr12:49318695-49318702 chr12:49318745-49318754 chr12:49318693-49318704 chr12:49318693-49318703 chr12:49318694-49318703 chr12:49318690-49318705 chr12:49318693-49318704 chr12:49318743-49318756 chr12:49318694-49318703 chr12:49318744-49318755 chr12:49318692-49318705 chr12:49318694-49318704
16	POLR2A	chr12:49318491-49319551	GM10847	blood:	n/a	n/a
17	POLR2A	chr12:49318182-49319869	GM12892	blood:	n/a	n/a
18	MXI1	chr12:49318401-49319081	H1-hESC	embryonic stem cell:	n/a	chr12:49318746-49318755
19	MAX	chr12:49318439-49318831	Hela-S3	cervix:	n/a	chr12:49318695-49318702 chr12:49318745-49318754 chr12:49318693-49318704 chr12:49318693-49318703 chr12:49318694-49318703 chr12:49318690-49318705 chr12:49318693-49318704 chr12:49318743-49318756 chr12:49318694-49318703 chr12:49318744-49318755 chr12:49318692-49318705 chr12:49318694-49318704
20	SIN3A	chr12:49318365-49319780	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr12:49318390-49319574	GM15510	blood:	n/a	n/a
22	STAT5A	chr12:49318066-49319746	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:49318783-49319618	PANC-1	pancreas:	n/a	n/a
24	ELF1	chr12:49318266-49318846	MCF-7	breast:	n/a	n/a
25	CHD2	chr12:49318448-49319687	GM12878	blood:	n/a	n/a
26	FOXM1	chr12:49318349-49319560	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:49317828-49319985	H1-hESC	embryonic stem cell:	n/a	n/a
28	E2F6	chr12:49318415-49318970	A549	lung:	n/a	chr12:49318513-49318523
29	USF1	chr12:49318394-49318940	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr12:49318352-49319741	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:49318419-49319559	GM18526	blood:	n/a	n/a
32	CTCF	chr12:49318216-49318814	MCF-7	breast:	n/a	n/a
33	POLR2A	chr12:49318270-49319815	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr12:49318287-49319692	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr12:49318272-49319694	HUVEC	blood vessel:	n/a	n/a
36	USF1	chr12:49318323-49318961	ECC-1	luminal epithelium:	n/a	n/a
37	MAX	chr12:49318272-49319752	H1-hESC	embryonic stem cell:	n/a	chr12:49318695-49318702 chr12:49318745-49318754 chr12:49318693-49318704 chr12:49318693-49318703 chr12:49318694-49318703 chr12:49318690-49318705 chr12:49318693-49318704 chr12:49318743-49318756 chr12:49318694-49318703 chr12:49318744-49318755 chr12:49318692-49318705 chr12:49318694-49318704
38	MYC	chr12:49318403-49318800	GM12878	blood:	n/a	chr12:49318695-49318702 chr12:49318745-49318754 chr12:49318693-49318704 chr12:49318693-49318703 chr12:49318694-49318703 chr12:49318690-49318705 chr12:49318693-49318704 chr12:49318743-49318756 chr12:49318694-49318703 chr12:49318744-49318755 chr12:49318692-49318705 chr12:49318694-49318704
39	CREB1	chr12:49318409-49319687	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr12:49318366-49319579	GM19193	blood:	n/a	n/a
41	POLR2A	chr12:49318796-49319832	GM12891	blood:	n/a	n/a
42	MAX	chr12:49318485-49319209	A549	lung:	n/a	chr12:49318695-49318702 chr12:49318745-49318754 chr12:49318693-49318704 chr12:49318693-49318703 chr12:49318694-49318703 chr12:49318690-49318705 chr12:49318693-49318704 chr12:49318743-49318756 chr12:49318694-49318703 chr12:49318744-49318755 chr12:49318692-49318705 chr12:49318694-49318704
43	POLR2A	chr12:49318406-49319536	GM12891	blood:	n/a	n/a
44	MAX	chr12:49318384-49318999	HepG2	liver:	n/a	chr12:49318695-49318702 chr12:49318745-49318754 chr12:49318693-49318704 chr12:49318693-49318703 chr12:49318694-49318703 chr12:49318690-49318705 chr12:49318693-49318704 chr12:49318743-49318756 chr12:49318694-49318703 chr12:49318744-49318755 chr12:49318692-49318705 chr12:49318694-49318704
45	BCL3	chr12:49318435-49319676	A549	lung:	n/a	n/a
46	MYC	chr12:49318177-49319865	A549	lung:	n/a	chr12:49318695-49318702 chr12:49318745-49318754 chr12:49318693-49318704 chr12:49318693-49318703 chr12:49318694-49318703 chr12:49318690-49318705 chr12:49318693-49318704 chr12:49318743-49318756 chr12:49318694-49318703 chr12:49318744-49318755 chr12:49318692-49318705 chr12:49318694-49318704
47	POLR2A	chr12:49318376-49319627	GM18505	blood:	n/a	n/a
48	POLR2A	chr12:49318300-49319781	GM12878	blood:	n/a	n/a
49	POLR2A	chr12:49318790-49319744	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr12:49318785-49319560	HUVEC	blood vessel:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:49318784-49318834	MCF-7	breast:	n/a
2	chr12:49318784-49318834	HCPEpiC	choroid plexus:	n/a
3	chr12:49318784-49318834	AG04449	skin:	fetal
4	chr12:49318784-49318834	BJ	skin:	n/a
5	chr12:49318784-49318834	HRPEpiC	eye:	n/a
6	chr12:49318784-49318834	IMR90	lung:	fetal
7	chr12:49318784-49318834	AG09309	skin:	n/a
8	chr12:49318784-49318834	HAEpiC	amniotic membrane:	n/a
9	chr12:49318784-49318834	GM06990	blood:	n/a
10	chr12:49318784-49318834	PrEC	prostate:	n/a
11	chr12:49318784-49318834	HL-60	blood:	n/a
12	chr12:49318784-49318834	H1-hESC	embryonic stem cell:	embryo
13	chr12:49318784-49318834	SK-N-SH	brain:	n/a
14	chr12:49318784-49318834	SKMC	muscle:	n/a
15	chr12:49318784-49318834	HPAEpiC	pulmonary alveolar:	n/a
16	chr12:49318784-49318834	HIPEpiC	eye:	n/a
17	chr12:49318784-49318834	HNPCEpiC	eye:	n/a
18	chr12:49318784-49318834	Hepatocyte	liver:	n/a
19	chr12:49318784-49318834	GM19239	blood:	n/a
20	chr12:49318784-49318834	HCT-116	colon:	n/a
21	chr12:49318784-49318834	PFSK-1	brain:	n/a
22	chr12:49318784-49318834	AG10803	skin:	n/a
23	chr12:49318784-49318834	HRE	kidney:	n/a
24	chr12:49318784-49318834	MCF10A-Er-Src	breast:	n/a
25	chr12:49318784-49318834	AoSMC	blood vessel:	n/a
26	chr12:49318784-49318834	Caco-2	colon:	n/a
27	chr12:49318784-49318834	U87	brain:	n/a
28	chr12:49318784-49318834	Hela-S3	cervix:	n/a
29	chr12:49318784-49318834	SAEC	small airway:	n/a
30	chr12:49318784-49318834	NB4	blood:	n/a
31	chr12:49318784-49318834	HMEC	breast:	n/a
32	chr12:49318784-49318834	T-47D	breast:	n/a
33	chr12:49318784-49318834	NH-A	brain:	n/a
34	chr12:49318784-49318834	ProgFib	skin:	n/a
35	chr12:49318784-49318834	HCM	heart:	n/a
36	chr12:49318784-49318834	HCF	heart:	n/a
37	chr12:49318784-49318834	HRCEpiC	kidney:	n/a
38	chr12:49318784-49318834	CMK	blood:	n/a
39	chr12:49318784-49318834	K562	blood:	n/a
40	chr12:49318784-49318834	NHDF-neo	bronchial:	n/a
41	chr12:49318784-49318834	GM12892	blood:	n/a
42	chr12:49318784-49318834	ECC-1	luminal epithelium:	n/a
43	chr12:49318784-49318834	RPTEC	kidney:	n/a
44	chr12:49318784-49318834	SK-N-SH_RA	brain:	n/a
45	chr12:49318784-49318834	NT2-D1	testis:	n/a
46	chr12:49318784-49318834	HUVEC	blood vessel:	n/a
47	chr12:49318784-49318834	AG09319	gingival:	n/a
48	chr12:49318784-49318834	HEK293	kidney:	embryo
49	chr12:49318784-49318834	ovcar-3	ovarian:	n/a
50	chr12:49318784-49318834	Jurkat	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49211386..49213758-chr12:49317822..49319346,2	MCF-7	breast:
2	chr12:49316917..49319846-chr12:49321799..49325494,4	K562	blood:
3	chr12:49317412..49320697-chr12:49349793..49352537,4	MCF-7	breast:
4	chr12:49318409..49320473-chr12:49386787..49389154,2	MCF-7	breast:
5	chr12:49257454..49260772-chr12:49317154..49320539,3	MCF-7	breast:
6	chr12:49245963..49247751-chr12:49317835..49320703,2	MCF-7	breast:
7	chr12:49258143..49260662-chr12:49316104..49319150,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FKBP11-1	chr12:49318609-49318905	NONHSAT028048

Variant related genes	Relation type
FKBP11	TF binding region
FKBP11	CpG island
ENSG00000201678	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000172602	Chromatin interaction
ENSG00000258283	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000134287	Chromatin interaction
ENSG00000272822	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11610308	1.00[CHB][hapmap]
rs11833860	1.00[CHB][hapmap]
rs12318558	1.00[CHB][hapmap]
rs3741624	1.00[CHB][hapmap]
rs6580694	1.00[CHD][hapmap]
rs833823	1.00[CHB][hapmap]
rs953673	1.00[CHD][hapmap]

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	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription 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 target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:136 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49313400-49319000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:49314400-49338000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:49314400-49338600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:49315800-49321000	Weak transcription	K562	blood
5	chr12:49317200-49319400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
6	chr12:49317800-49319400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:49317800-49319400	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr12:49318000-49318800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:49318000-49319400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:49318000-49319400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:49318000-49319400	Active TSS	Rectal Smooth Muscle	rectum
12	chr12:49318000-49319800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr12:49318200-49318800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr12:49318200-49318800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:49318200-49318800	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr12:49318200-49318800	Flanking Active TSS	NHLF	lung
17	chr12:49318200-49319000	Active TSS	Fetal Brain Female	brain
18	chr12:49318200-49319200	Active TSS	Monocytes-CD14+_RO01746	blood
19	chr12:49318200-49319400	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr12:49318200-49319400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
21	chr12:49318200-49319400	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr12:49318200-49319400	Active TSS	Gastric	stomach
23	chr12:49318200-49319600	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr12:49318200-49319800	Active TSS	H9 Cell Line	embryonic stem cell
25	chr12:49318200-49319800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:49318200-49319800	Active TSS	Right Ventricle	heart
27	chr12:49318400-49318800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr12:49318400-49319000	Active TSS	A549	lung
29	chr12:49318400-49319200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr12:49318400-49319200	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr12:49318400-49319200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:49318400-49319200	Active TSS	Pancreas	Pancrea
33	chr12:49318400-49319200	Active TSS	Placenta Amnion	Placenta Amnion
34	chr12:49318400-49319400	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr12:49318400-49319400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:49318400-49319400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:49318400-49319400	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr12:49318400-49319400	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr12:49318400-49319400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:49318400-49319400	Active TSS	Primary B cells from cord blood	blood
41	chr12:49318400-49319400	Active TSS	Primary hematopoietic stem cells	blood
42	chr12:49318400-49319400	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr12:49318400-49319400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:49318400-49319400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr12:49318400-49319400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:49318400-49319400	Active TSS	Brain Angular Gyrus	brain
47	chr12:49318400-49319400	Active TSS	Brain Substantia Nigra	brain
48	chr12:49318400-49319400	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr12:49318400-49319400	Active TSS	Esophagus	oesophagus
50	chr12:49318400-49319400	Active TSS	Fetal Intestine Large	intestine

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