Variant report

Variant	rs17123751
Chromosome Location	chr12:49945549-49945550
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	BHLHE40	chr12:49945410-49945650	HepG2	liver:	n/a	n/a
2	USF1	chr12:49945350-49945662	K562	blood:	n/a	chr12:49945451-49945462
3	ATF1	chr12:49945439-49945688	K562	blood:	n/a	n/a
4	USF1	chr12:49945369-49945568	HepG2	liver:	n/a	chr12:49945451-49945462
5	E2F6	chr12:49945385-49945637	K562	blood:	n/a	chr12:49945442-49945454
6	RCOR1	chr12:49945441-49945652	K562	blood:	n/a	n/a
7	MAX	chr12:49945417-49945600	NB4	blood:	n/a	chr12:49945452-49945462
8	MAX	chr12:49945367-49945673	K562	blood:	n/a	chr12:49945452-49945462
9	MAX	chr12:49945397-49945605	HepG2	liver:	n/a	chr12:49945452-49945462
10	MAX	chr12:49945374-49945758	HepG2	liver:	n/a	chr12:49945452-49945462
11	MAX	chr12:49945367-49945748	K562	blood:	n/a	chr12:49945452-49945462
12	MAX	chr12:49945371-49945666	K562	blood:	n/a	chr12:49945452-49945462
13	MYC	chr12:49945382-49945628	K562	blood:	n/a	chr12:49945452-49945462
14	BHLHE40	chr12:49945363-49945750	K562	blood:	n/a	n/a
15	JUND	chr12:49945415-49945646	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49936026..49937572-chr12:49942956..49945602,2	K562	blood:
2	chr12:49931274..49936005-chr12:49943051..49946094,6	K562	blood:
3	chr12:49758090..49761584-chr12:49941577..49946568,5	K562	blood:
4	chr12:49943184..49945945-chr12:49954748..49957080,2	K562	blood:
5	chr12:49751652..49753249-chr12:49945364..49947473,2	MCF-7	breast:

Variant related genes	Relation type
KCNH3	TF binding region
ENSG00000135519	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10506284	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10506285	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11169016	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11169048	1.00[CHB][hapmap]
rs11169058	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11169059	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11834161	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12296440	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12301632	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12305716	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12306118	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12309053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12310129	1.00[JPT][hapmap]
rs12315996	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12322561	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17123696	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs17123790	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123865	1.00[ASW][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap]
rs17123919	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17123922	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17197593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17198090	0.85[GIH][hapmap]
rs17198118	0.85[GIH][hapmap]
rs2272478	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4144469	1.00[JPT][hapmap]
rs4569075	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580707	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6580709	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6580716	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7139061	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7294648	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7294973	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7295162	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7309997	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7342365	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7955541	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7962951	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7969099	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7976165	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9919739	0.82[AFR][1000 genomes]
rs9919740	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs9919807	0.84[AFR][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	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv899071	chr12:49927148-49955935	Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49942600-49946600	Enhancers	Pancreas	Pancrea
2	chr12:49943000-49945600	Weak transcription	HMEC	breast
3	chr12:49943000-49950400	Weak transcription	GM12878-XiMat	blood
4	chr12:49943200-49945800	Weak transcription	Psoas Muscle	Psoas
5	chr12:49943200-49947200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr12:49943200-49951000	Weak transcription	Aorta	Aorta
7	chr12:49943200-49959600	Weak transcription	Right Atrium	heart
8	chr12:49943400-49949400	Weak transcription	Gastric	stomach
9	chr12:49943400-49949400	Weak transcription	Spleen	Spleen
10	chr12:49943400-49950000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr12:49943400-49950200	Weak transcription	Primary B cells from cord blood	blood
12	chr12:49943400-49952600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:49943600-49945600	Weak transcription	Brain Anterior Caudate	brain
14	chr12:49943600-49945600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:49943600-49945600	Weak transcription	Fetal Heart	heart
16	chr12:49943600-49945600	Enhancers	Fetal Intestine Small	intestine
17	chr12:49943600-49946000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr12:49943600-49946200	Enhancers	Fetal Intestine Large	intestine
19	chr12:49943600-49946400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr12:49943600-49947600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr12:49943600-49949800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr12:49943600-49949800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:49943600-49949800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:49943600-49949800	Weak transcription	Fetal Lung	lung
25	chr12:49943600-49950000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:49943600-49950000	Weak transcription	Ovary	ovary
27	chr12:49943600-49950200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr12:49943600-49950200	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:49943600-49950400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:49943800-49945800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:49943800-49946000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:49944200-49952200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:49944400-49945600	Weak transcription	Fetal Brain Female	brain
34	chr12:49944400-49946800	Enhancers	Liver	Liver
35	chr12:49944600-49945600	Weak transcription	Brain Angular Gyrus	brain
36	chr12:49944600-49945600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr12:49944600-49945600	Weak transcription	Brain Substantia Nigra	brain
38	chr12:49944800-49945800	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:49944800-49947600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:49944800-49949800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr12:49944800-49952400	Weak transcription	Fetal Kidney	kidney
42	chr12:49945000-49949400	Weak transcription	Thymus	Thymus
43	chr12:49945000-49952400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:49945200-49947200	Enhancers	HepG2	liver
45	chr12:49945200-49949800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:49945400-49945600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:49945400-49945600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
48	chr12:49945400-49945800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:49945400-49945800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
50	chr12:49945400-49946000	Enhancers	Fetal Brain Male	brain

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