Variant report

Variant	rs12424035
Chromosome Location	chr12:50303414-50303415
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr12:50303227-50304348	MCF-7	breast:	n/a	n/a
2	MAX	chr12:50303243-50304154	H1-hESC	embryonic stem cell:	n/a	n/a
3	EGR1	chr12:50303296-50304092	MCF-7	breast:	n/a	n/a
4	MAX	chr12:50303394-50304223	MCF-7	breast:	n/a	n/a
5	MAZ	chr12:50303298-50304105	IMR90	lung:	n/a	n/a
6	E2F6	chr12:50303291-50303426	K562	blood:	n/a	n/a
7	E2F6	chr12:50303348-50304105	K562	blood:	n/a	n/a
8	ZNF263	chr12:50303165-50303952	HEK293-T-REx	kidney:	n/a	n/a
9	EGR1	chr12:50303403-50304185	HCT-116	colon:	n/a	n/a
10	SMARCB1	chr12:50303265-50304193	Hela-S3	cervix:	n/a	n/a
11	NR2F2	chr12:50303411-50304407	MCF-7	breast:	n/a	n/a
12	POLR2A	chr12:50303408-50304078	SK-N-MC	brain:	n/a	n/a
13	MAX	chr12:50303354-50304427	HCT-116	colon:	n/a	n/a
14	ZNF143	chr12:50303371-50303888	Hela-S3	cervix:	n/a	n/a
15	MAX	chr12:50303179-50304361	ECC-1	luminal epithelium:	n/a	n/a
16	E2F6	chr12:50303073-50304853	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr12:50303359-50304397	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50302143..50304526-chr12:50326820..50329441,2	K562	blood:
2	chr12:50259475..50261235-chr12:50302095..50303974,2	MCF-7	breast:
3	chr12:50287995..50291255-chr12:50301230..50303586,3	MCF-7	breast:
4	chr12:50301650..50304024-chr12:50450316..50452712,2	MCF-7	breast:
5	chr12:50280749..50283185-chr12:50302000..50304856,3	MCF-7	breast:
6	chr12:50303280..50304785-chr12:50307920..50310046,2	K562	blood:
7	chr12:50295593..50300153-chr12:50302401..50306371,6	MCF-7	breast:
8	chr12:50302479..50304923-chr12:50336805..50339549,2	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAIM2-1	chr12:50302668-50304837	XLOC_010072
2	lnc-FAIM2-1	chr12:50302676-50304837	ENSG00000258135
3	lnc-FAIM2-1	chr12:50302666-50304837	NONHSAT028150

No data

Variant related genes	Relation type
ENSG00000257771	TF binding region
ENSG00000110881	Chromatin interaction
ENSG00000135472	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12306966	0.83[AFR][1000 genomes]
rs12312614	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12422556	0.83[ASN][1000 genomes]
rs12422575	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12424268	0.84[ASN][1000 genomes]
rs12424404	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12426614	1.00[CEU][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426750	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12427024	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12427051	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17124131	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs184172	0.92[ASN][1000 genomes]
rs2276187	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2298640	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2298641	1.00[CEU][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55984325	0.91[EUR][1000 genomes]
rs58494052	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59862432	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61416142	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72644872	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72644873	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72644874	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72644875	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72644876	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS 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 target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer 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	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription 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	36 gene(s)	inside rSNPs	diseases
7	nsv525920	chr12:50285061-50304949	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv558836	chr12:50290023-50316439	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50298200-50307800	Weak transcription	Right Atrium	heart
2	chr12:50298400-50308000	Weak transcription	Pancreas	Pancrea
3	chr12:50302800-50304800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:50302800-50305200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
5	chr12:50303000-50303800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:50303000-50304000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr12:50303000-50304000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:50303000-50304400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:50303000-50304400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:50303000-50304400	Enhancers	K562	blood
11	chr12:50303000-50304600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr12:50303000-50304600	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr12:50303200-50303800	Enhancers	Fetal Heart	heart
14	chr12:50303200-50304200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:50303200-50304200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
16	chr12:50303200-50304200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr12:50303200-50304200	Enhancers	NH-A	brain
18	chr12:50303200-50304400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:50303200-50304400	Enhancers	HMEC	breast
20	chr12:50303200-50304600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:50303200-50304600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
22	chr12:50303200-50304800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:50303200-50304800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:50303200-50304800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:50303200-50306400	Enhancers	H1 Cell Line	embryonic stem cell
26	chr12:50303400-50303600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:50303400-50303600	Enhancers	Fetal Lung	lung
28	chr12:50303400-50303600	Bivalent Enhancer	Fetal Muscle Leg	muscle
29	chr12:50303400-50303800	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr12:50303400-50304000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
31	chr12:50303400-50304000	Enhancers	Brain Germinal Matrix	brain
32	chr12:50303400-50304000	Bivalent Enhancer	HepG2	liver
33	chr12:50303400-50304000	Enhancers	NHEK	skin
34	chr12:50303400-50304200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr12:50303400-50304200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:50303400-50304200	Flanking Active TSS	Hela-S3	cervix
37	chr12:50303400-50304200	Enhancers	HUVEC	blood vessel
38	chr12:50303400-50304400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:50303400-50304400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
40	chr12:50303400-50304400	Enhancers	Stomach Mucosa	stomach
41	chr12:50303400-50304600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:50303400-50311800	Weak transcription	Gastric	stomach

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