Variant report

Variant	rs12424404
Chromosome Location	chr12:50297375-50297376
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	POLR2A	chr12:50297293-50298261	U87	brain:	n/a	n/a
2	MAZ	chr12:50297162-50298795	IMR90	lung:	n/a	chr12:50298120-50298129
3	JUND	chr12:50296797-50298438	SK-N-SH	brain:	n/a	n/a
4	MXI1	chr12:50296732-50298603	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr12:50297340-50297490	BE2_C	brain:	n/a	n/a
6	RCOR1	chr12:50297345-50297721	K562	blood:	n/a	n/a
7	REST	chr12:50297242-50298354	H1-neurons	neurons:	n/a	chr12:50297684-50297697 chr12:50298151-50298169 chr12:50297684-50297697

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50295593..50300153-chr12:50302401..50306371,6	MCF-7	breast:
2	chr12:50290402..50293463-chr12:50294998..50297478,3	MCF-7	breast:

Variant related genes	Relation type
FAIM2	TF binding region
ENSG00000257771	Chromatin interaction
ENSG00000135472	Chromatin interaction
ENSG00000258135	Chromatin interaction

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

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

rs_ID	r²[population]
rs12312614	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12422556	0.88[AMR][1000 genomes]
rs12422575	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12424035	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12424268	1.00[AMR][1000 genomes]
rs12426614	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12426750	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12427024	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12427051	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17124129	1.00[AMR][1000 genomes]
rs17124131	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs184172	0.86[ASN][1000 genomes]
rs2276187	0.91[EUR][1000 genomes]
rs2298640	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2298641	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55984325	0.91[EUR][1000 genomes]
rs58494052	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59862432	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61416142	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72644872	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72644873	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72644874	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72644875	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72644876	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[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:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50292000-50297400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr12:50295200-50303000	Weak transcription	K562	blood
3	chr12:50295600-50297800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:50296200-50297400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:50296200-50297400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:50296400-50298000	Active TSS	Brain Anterior Caudate	brain
7	chr12:50296400-50298000	Active TSS	Brain Cingulate Gyrus	brain
8	chr12:50296400-50298200	Active TSS	Brain Hippocampus Middle	brain
9	chr12:50296400-50298200	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr12:50296600-50297600	Flanking Active TSS	Fetal Brain Male	brain
11	chr12:50296600-50298000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:50296600-50298000	Active TSS	Brain Angular Gyrus	brain
13	chr12:50296800-50297400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:50296800-50297400	Enhancers	Ovary	ovary
15	chr12:50296800-50297400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
16	chr12:50296800-50297400	Enhancers	NH-A	brain
17	chr12:50296800-50297600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
18	chr12:50296800-50298000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:50296800-50298200	Active TSS	Brain Germinal Matrix	brain
20	chr12:50296800-50298200	Active TSS	Brain Substantia Nigra	brain
21	chr12:50297000-50297400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:50297000-50297400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
23	chr12:50297000-50297400	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr12:50297000-50297400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:50297000-50297400	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr12:50297000-50297400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:50297000-50297400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
28	chr12:50297000-50297600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr12:50297000-50297800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr12:50297000-50298000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
31	chr12:50297000-50298000	Active TSS	Rectal Smooth Muscle	rectum
32	chr12:50297000-50298200	Active TSS	Right Atrium	heart
33	chr12:50297000-50298200	Active TSS	Right Ventricle	heart
34	chr12:50297000-50298400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
35	chr12:50297000-50298400	Bivalent/Poised TSS	Left Ventricle	heart
36	chr12:50297200-50297400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
37	chr12:50297200-50297400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:50297200-50297400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:50297200-50297400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:50297200-50297400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr12:50297200-50297400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr12:50297200-50297400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr12:50297200-50297400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:50297200-50297400	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr12:50297200-50297600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr12:50297200-50297600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:50297200-50297600	Flanking Active TSS	Fetal Brain Female	brain
48	chr12:50297200-50297600	Flanking Active TSS	NHLF	lung
49	chr12:50297200-50297800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:50297200-50298000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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