Variant report

Variant	rs393848
Chromosome Location	chr12:50466085-50466086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr12:50465986-50466330	K562	blood:	n/a	chr12:50466102-50466115
2	NR2F2	chr12:50465916-50466314	K562	blood:	n/a	n/a
3	ARID3A	chr12:50465998-50466144	K562	blood:	n/a	n/a
4	UBTF	chr12:50466061-50466200	K562	blood:	n/a	n/a
5	NR2F2	chr12:50465943-50466276	K562	blood:	n/a	n/a
6	JUND	chr12:50466043-50466162	K562	blood:	n/a	n/a
7	ZBTB7A	chr12:50465971-50466283	K562	blood:	n/a	n/a
8	EGR1	chr12:50465974-50466256	K562	blood:	n/a	chr12:50466102-50466115
9	MAZ	chr12:50465974-50466268	K562	blood:	n/a	n/a
10	HDAC2	chr12:50466042-50466206	K562	blood:	n/a	n/a
11	RCOR1	chr12:50465984-50466283	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50465226..50467523-chr12:50469793..50471990,2	K562	blood:
2	chr12:50464486..50466222-chr12:50466787..50469329,2	K562	blood:
3	chr12:50465539..50467962-chr12:50472151..50474107,2	K562	blood:
4	chr12:50259278..50261065-chr12:50464788..50467159,2	K562	blood:
5	chr12:50464456..50466840-chr12:50477683..50480596,2	MCF-7	breast:
6	chr12:50464941..50466532-chr12:50496358..50498847,2	MCF-7	breast:
7	chr12:50359856..50363195-chr12:50464299..50467277,4	MCF-7	breast:

No data

Variant related genes	Relation type
ASIC1	TF binding region
ENSG00000066117	Chromatin interaction
ENSG00000167588	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000086159	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs376184	0.91[ASN][1000 genomes]
rs386469	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs404751	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs439171	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs450423	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs484951	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4898546	0.80[ASN][1000 genomes]
rs590460	0.81[ASN][1000 genomes]
rs613066	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs627869	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs627887	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs653576	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs706789	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs706794	0.91[ASN][1000 genomes]
rs835591	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs835593	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs835594	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs836184	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836185	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836186	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs844359	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs860699	0.88[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	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
4	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS 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	28 gene(s)	inside rSNPs	diseases
6	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50458200-50478200	Weak transcription	Thymus	Thymus
2	chr12:50460600-50469200	Weak transcription	Psoas Muscle	Psoas
3	chr12:50460600-50469400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:50460800-50469200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:50461000-50468800	Weak transcription	HSMMtube	muscle
6	chr12:50464000-50467000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr12:50464400-50466800	Weak transcription	Fetal Kidney	kidney
8	chr12:50464400-50467400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:50464400-50467600	Weak transcription	HepG2	liver
10	chr12:50464400-50468800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:50464400-50469200	Weak transcription	Brain Substantia Nigra	brain
12	chr12:50464400-50469200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr12:50464400-50469200	Weak transcription	Fetal Lung	lung
14	chr12:50464400-50469200	Weak transcription	Pancreas	Pancrea
15	chr12:50464400-50478200	Weak transcription	Fetal Heart	heart
16	chr12:50464400-50478200	Weak transcription	Right Atrium	heart
17	chr12:50464600-50467000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:50464600-50468800	Weak transcription	Liver	Liver
19	chr12:50464600-50469200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:50464600-50469600	Weak transcription	Colonic Mucosa	Colon
21	chr12:50464800-50466400	Weak transcription	Fetal Brain Male	brain
22	chr12:50464800-50466800	Enhancers	K562	blood
23	chr12:50464800-50468600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:50464800-50468600	Weak transcription	Fetal Intestine Large	intestine
25	chr12:50464800-50468800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:50464800-50468800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:50464800-50468800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr12:50464800-50468800	Weak transcription	Fetal Intestine Small	intestine
29	chr12:50464800-50468800	Weak transcription	Gastric	stomach
30	chr12:50464800-50468800	Weak transcription	Right Ventricle	heart
31	chr12:50464800-50468800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:50464800-50468800	Weak transcription	NH-A	brain
33	chr12:50464800-50469000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:50464800-50469000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr12:50464800-50469000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:50464800-50469000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:50464800-50469000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:50464800-50469000	Weak transcription	Stomach Mucosa	stomach
39	chr12:50464800-50469200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr12:50464800-50469200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:50464800-50469200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr12:50464800-50469200	Weak transcription	Brain Angular Gyrus	brain
43	chr12:50464800-50469200	Weak transcription	Brain Anterior Caudate	brain
44	chr12:50464800-50469200	Weak transcription	Brain Hippocampus Middle	brain
45	chr12:50464800-50469200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:50464800-50469200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr12:50464800-50469200	Weak transcription	HMEC	breast
48	chr12:50464800-50471600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:50464800-50474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:50464800-50478200	Weak transcription	Colon Smooth Muscle	Colon

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