Variant report

Variant	rs12071124
Chromosome Location	chr1:241683705-241683706
allele	A/C
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	IRF1	chr1:241682771-241684009	K562	blood:	n/a	chr1:241683832-241683842 chr1:241683595-241683609 chr1:241683060-241683074 chr1:241683592-241683605 chr1:241683928-241683937 chr1:241683927-241683936
2	GATA1	chr1:241682043-241683932	PBDE	blood:	n/a	chr1:241683246-241683257 chr1:241683570-241683579
3	CUX1	chr1:241682822-241683763	K562	blood:	n/a	n/a
4	ZNF143	chr1:241682675-241683729	K562	blood:	n/a	chr1:241683252-241683267 chr1:241682861-241682879 chr1:241683251-241683270
5	MYC	chr1:241682940-241683872	MCF10A-Er-Src	breast:	n/a	chr1:241683182-241683192
6	PML	chr1:241682294-241683786	K562	blood:	n/a	n/a
7	MXI1	chr1:241681747-241684092	SK-N-SH	brain:	n/a	n/a
8	EP300	chr1:241682879-241683912	K562	blood:	n/a	chr1:241683828-241683842 chr1:241683789-241683798
9	HCFC1	chr1:241682603-241684410	Hela-S3	cervix:	n/a	n/a
10	MYC	chr1:241682646-241683872	MCF10A-Er-Src	breast:	n/a	chr1:241683182-241683192 chr1:241682862-241682872
11	BRCA1	chr1:241682758-241684056	Hela-S3	cervix:	n/a	n/a
12	TBL1XR1	chr1:241682889-241684119	K562	blood:	n/a	n/a
13	TBP	chr1:241682846-241684360	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr1:241683278-241684065	K562	blood:	n/a	n/a
15	REST	chr1:241682316-241683763	H1-neurons	neurons:	n/a	chr1:241682606-241682619 chr1:241682628-241682638
16	POLR2A	chr1:241681074-241683713	MCF10A-Er-Src	breast:	n/a	n/a
17	ARID3A	chr1:241683097-241684070	K562	blood:	n/a	n/a
18	JUN	chr1:241682809-241683724	K562	blood:	n/a	n/a
19	IRF1	chr1:241682692-241683738	K562	blood:	n/a	chr1:241683595-241683609 chr1:241683060-241683074 chr1:241683592-241683605

No.	Distal block	Cell Line	Cell type
1	chr1:241683433..241685881-chr1:241689141..241691385,3	MCF-7	breast:
2	chr1:241681898..241684060-chr1:242010602..242013002,4	K562	blood:
3	chr1:241680902..241684541-chr1:242009942..242012706,4	K562	blood:

Variant related genes	Relation type
FH	TF binding region
ENSG00000174371	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10926507	0.86[EUR][1000 genomes]
rs12120348	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1414493	0.86[EUR][1000 genomes]
rs2153694	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2994982	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2994985	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2994987	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2994989	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4310432	0.85[EUR][1000 genomes]
rs4659607	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4660100	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6678766	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6679290	0.86[EUR][1000 genomes]
rs7530270	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv949442	chr1:241432051-241730054	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking 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	27 gene(s)	inside rSNPs	diseases
6	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv873371	chr1:241667244-241747838	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv3394983	chr1:241681554-241684102	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241680600-241684000	Active TSS	A549	lung
2	chr1:241680800-241684000	Active TSS	HMEC	breast
3	chr1:241681200-241683800	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr1:241681200-241683800	Active TSS	NH-A	brain
5	chr1:241681200-241684000	Active TSS	NHDF-Ad	bronchial
6	chr1:241681400-241683800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:241681400-241683800	Active TSS	GM12878-XiMat	blood
8	chr1:241681400-241684000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:241681600-241683800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:241681600-241683800	Active TSS	Fetal Intestine Large	intestine
11	chr1:241681600-241683800	Active TSS	Fetal Muscle Leg	muscle
12	chr1:241681600-241683800	Active TSS	Hela-S3	cervix
13	chr1:241681600-241684000	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr1:241681600-241684000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:241681800-241683800	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr1:241681800-241683800	Active TSS	Stomach Smooth Muscle	stomach
17	chr1:241681800-241684000	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr1:241681800-241684000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:241682000-241683800	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr1:241682000-241683800	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr1:241682000-241683800	Active TSS	Brain Anterior Caudate	brain
22	chr1:241682000-241683800	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr1:241682000-241683800	Active TSS	Colon Smooth Muscle	Colon
24	chr1:241682000-241683800	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr1:241682000-241683800	Active TSS	NHEK	skin
26	chr1:241682000-241683800	Active TSS	Osteobl	bone
27	chr1:241682000-241684200	Active TSS	Duodenum Mucosa	Duodenum
28	chr1:241682000-241684200	Active TSS	K562	blood
29	chr1:241682200-241683800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:241682200-241683800	Active TSS	Brain Cingulate Gyrus	brain
31	chr1:241682200-241683800	Active TSS	Brain Germinal Matrix	brain
32	chr1:241682200-241683800	Active TSS	Fetal Kidney	kidney
33	chr1:241682200-241683800	Active TSS	Fetal Stomach	stomach
34	chr1:241682200-241683800	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr1:241682200-241683800	Active TSS	Rectal Smooth Muscle	rectum
36	chr1:241682200-241684000	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr1:241682200-241684000	Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr1:241682200-241684000	Active TSS	Fetal Brain Female	brain
39	chr1:241682400-241683800	Active TSS	Primary B cells from peripheral blood	blood
40	chr1:241682400-241683800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr1:241682400-241683800	Active TSS	Brain Angular Gyrus	brain
42	chr1:241682400-241683800	Active TSS	Brain Hippocampus Middle	brain
43	chr1:241682400-241683800	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr1:241682400-241683800	Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr1:241682400-241684000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:241682400-241684000	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr1:241682400-241684000	Active TSS	Thymus	Thymus
48	chr1:241682400-241684200	Active TSS	HepG2	liver
49	chr1:241682600-241683800	Active TSS	Primary monocytes fromperipheralblood	blood
50	chr1:241682600-241683800	Active TSS	Primary T cells fromperipheralblood	blood

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