Variant report

Variant	rs57739230
Chromosome Location	chr12:104162745-104162746
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:104162700-104162850	MCF-7	breast:	n/a	n/a
2	CTCF	chr12:104162588-104162749	MCF-7	breast:	n/a	n/a
3	CTCF	chr12:104162574-104162765	MCF-7	breast:	n/a	n/a
4	CTCF	chr12:104162640-104162790	WERI-Rb-1	eye:	n/a	n/a
5	CTCF	chr12:104162635-104162762	MCF-7	breast:	n/a	n/a
6	CTCF	chr12:104162720-104162870	HBMEC	blood vessel:	n/a	n/a
7	CTCF	chr12:104162660-104162810	HepG2	liver:	n/a	n/a
8	CTCF	chr12:104162600-104162750	HPAF	blood vessel:	n/a	n/a
9	CHD2	chr12:104162607-104163022	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr12:104162640-104162790	AG04449	skin:	n/a	n/a
11	CTCF	chr12:104162600-104162750	MCF-7	breast:	n/a	n/a
12	CTCF	chr12:104162680-104162830	HEK293	kidney:	n/a	n/a
13	CTCF	chr12:104162620-104162770	HAc	cerebellar:	n/a	n/a
14	RAD21	chr12:104162439-104162928	A549	lung:	n/a	n/a
15	CTCF	chr12:104162605-104162767	MCF-7	breast:	n/a	n/a
16	CTCF	chr12:104162600-104162750	HCPEpiC	choroid plexus:	n/a	n/a
17	CTCF	chr12:104162600-104162750	HMF	breast:	n/a	n/a
18	RAD21	chr12:104162559-104162821	SK-N-SH_RA	brain:	n/a	n/a
19	RAD21	chr12:104162454-104162889	MCF-7	breast:	n/a	n/a
20	CTCF	chr12:104162597-104162756	HepG2	liver:	n/a	n/a
21	MAX	chr12:104162676-104163411	NB4	blood:	n/a	chr12:104163085-104163094
22	CTCF	chr12:104162620-104162770	AG09319	gingival:	n/a	n/a
23	CTCF	chr12:104162536-104162761	A549	lung:	n/a	n/a
24	CTCF	chr12:104162640-104162790	NB4	blood:	n/a	n/a
25	CTCF	chr12:104162628-104162748	MCF-7	breast:	n/a	n/a
26	CTCF	chr12:104162620-104162770	HCPEpiC	choroid plexus:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104160749..104162806-chr12:104234443..104236279,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257681	TF binding region
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11111780	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12312058	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1370782	0.87[ASN][1000 genomes]
rs17034527	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17034633	0.84[ASN][1000 genomes]
rs17034635	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4964571	0.86[ASN][1000 genomes]
rs57412476	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57498429	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs59509226	0.84[ASN][1000 genomes]
rs60828015	0.93[ASN][1000 genomes]
rs6539102	0.86[ASN][1000 genomes]
rs7132446	0.84[ASN][1000 genomes]
rs7135803	0.84[ASN][1000 genomes]
rs884394	0.89[ASN][1000 genomes]
rs934844	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899486	chr12:104118587-104170474	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv899491	chr12:104151560-104175575	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv899492	chr12:104151560-104183658	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104145800-104166800	Weak transcription	Right Atrium	heart
2	chr12:104146200-104169400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:104147000-104165400	Strong transcription	Stomach Smooth Muscle	stomach
4	chr12:104150000-104166800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:104151600-104170400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:104152400-104162800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:104152600-104162800	Weak transcription	Psoas Muscle	Psoas
8	chr12:104152600-104171200	Weak transcription	Esophagus	oesophagus
9	chr12:104152800-104162800	Weak transcription	Brain Angular Gyrus	brain
10	chr12:104152800-104165400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:104153200-104162800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:104153200-104185200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:104154400-104186400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:104154800-104170600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:104155000-104169000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr12:104155000-104170600	Weak transcription	Primary T cells from cord blood	blood
17	chr12:104155000-104170800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr12:104155000-104171000	Weak transcription	Osteobl	bone
19	chr12:104155000-104178000	Weak transcription	Colonic Mucosa	Colon
20	chr12:104155200-104162800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:104155200-104163200	Weak transcription	NHLF	lung
22	chr12:104155200-104173400	Weak transcription	NHDF-Ad	bronchial
23	chr12:104155600-104162800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:104155800-104169000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:104156000-104170800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:104156200-104170600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:104156600-104166600	Weak transcription	Brain Anterior Caudate	brain
28	chr12:104157400-104166400	Weak transcription	HSMMtube	muscle
29	chr12:104157400-104169000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:104157400-104172400	Weak transcription	GM12878-XiMat	blood
31	chr12:104157400-104191200	Weak transcription	HUVEC	blood vessel
32	chr12:104157600-104168800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:104157600-104170200	Weak transcription	K562	blood
34	chr12:104157800-104170600	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr12:104158200-104170400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:104158600-104170600	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr12:104158600-104170600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:104159000-104166400	Weak transcription	Brain Substantia Nigra	brain
39	chr12:104159200-104170400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:104159400-104162800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr12:104159400-104170400	Weak transcription	Fetal Brain Female	brain
42	chr12:104160200-104162800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr12:104160400-104162800	Weak transcription	Ovary	ovary
44	chr12:104160400-104162800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr12:104160400-104163000	Weak transcription	NHEK	skin
46	chr12:104160400-104165600	Weak transcription	Gastric	stomach
47	chr12:104160400-104166200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr12:104160400-104166200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:104160400-104166600	Weak transcription	Fetal Intestine Large	intestine
50	chr12:104160400-104170800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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