Variant report

Variant	rs12975641
Chromosome Location	chr19:40335059-40335060
allele	C/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	CTCF	chr19:40335000-40335150	BJ	skin:	n/a	n/a
2	MAX	chr19:40334506-40337825	A549	lung:	n/a	chr19:40337007-40337014 chr19:40337006-40337015
3	CTCF	chr19:40335020-40335170	GM12864	blood:	n/a	n/a
4	MYC	chr19:40334790-40338257	A549	lung:	n/a	chr19:40337007-40337014 chr19:40337006-40337015
5	POLR2A	chr19:40306432-40338982	PANC-1	pancreas:	n/a	n/a
6	CTCF	chr19:40334501-40335063	HCT-116	colon:	n/a	n/a
7	CTCF	chr19:40334654-40335061	K562	blood:	n/a	n/a
8	SIN3AK20	chr19:40332892-40340524	PANC-1	pancreas:	n/a	n/a
9	WRNIP1	chr19:40334426-40336849	GM12878	blood:	n/a	n/a
10	CTCF	chr19:40334289-40338535	A549	lung:	n/a	chr19:40336774-40336782 chr19:40336634-40336647
11	SIN3AK20	chr19:40334304-40340581	PANC-1	pancreas:	n/a	n/a
12	CTCF	chr19:40334920-40335070	K562	blood:	n/a	n/a
13	MXI1	chr19:40334712-40337666	IMR90	lung:	n/a	n/a
14	RAD21	chr19:40334435-40335077	SK-N-SH	brain:	n/a	n/a
15	RAD21	chr19:40334397-40335103	A549	lung:	n/a	n/a
16	CTCF	chr19:40334404-40335148	SK-N-SH	brain:	n/a	n/a
17	REST	chr19:40334688-40337514	PANC-1	pancreas:	n/a	chr19:40337343-40337363 chr19:40337343-40337363

No.	Distal block	Cell Line	Cell type
1	chr19:40327506..40332289-chr19:40333216..40337866,9	MCF-7	breast:
2	chr19:40321340..40326326-chr19:40333108..40338214,12	MCF-7	breast:
3	chr19:40283432..40284233-chr19:40334291..40335341,3	MCF-7	breast:
4	chr19:40283298..40284231-chr19:40334333..40335337,5	MCF-7	breast:
5	chr19:40029325..40030960-chr19:40334605..40336137,2	K562	blood:
6	chr19:40245446..40248757-chr19:40332343..40336010,3	MCF-7	breast:
7	chr19:40256350..40257493-chr19:40334257..40335289,4	MCF-7	breast:
8	chr19:39926041..39928299-chr19:40334872..40337810,2	MCF-7	breast:
9	chr19:40021563..40023552-chr19:40334495..40337354,2	K562	blood:
10	chr19:40333922..40335627-chr19:40352940..40355252,2	K562	blood:
11	chr19:40332530..40335412-chr19:40475463..40477228,2	MCF-7	breast:

Variant related genes	Relation type
FBL	TF binding region
ENSG00000196235	Chromatin interaction
ENSG00000105202	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000105204	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000013275	Chromatin interaction
ENSG00000105193	Chromatin interaction
ENSG00000269792	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10425638	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12975624	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12982808	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12982833	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803298	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv911696	chr19:40310497-40344648	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv9725	chr19:40315519-40412523	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40324800-40336000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:40329600-40335200	Weak transcription	Fetal Kidney	kidney
3	chr19:40329800-40335800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:40330800-40335200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr19:40330800-40335600	Weak transcription	Esophagus	oesophagus
6	chr19:40331000-40335200	Weak transcription	Brain Hippocampus Middle	brain
7	chr19:40331000-40335400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr19:40331400-40335200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:40331400-40335600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr19:40331400-40335600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr19:40331400-40335600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr19:40331400-40335800	Weak transcription	Colonic Mucosa	Colon
13	chr19:40331600-40335200	Weak transcription	Fetal Brain Female	brain
14	chr19:40332200-40335400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:40332200-40335600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:40332200-40336000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr19:40332200-40336000	Enhancers	Liver	Liver
18	chr19:40332400-40336000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr19:40332600-40335400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:40332600-40335600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr19:40333000-40335200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:40333000-40335600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr19:40333000-40335600	Enhancers	Duodenum Mucosa	Duodenum
24	chr19:40333000-40335800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr19:40333000-40336200	Enhancers	Placenta	Placenta
26	chr19:40333200-40335200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:40333200-40335200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:40333200-40335600	Enhancers	Primary T cells from cord blood	blood
29	chr19:40333200-40335600	Enhancers	Primary T cells fromperipheralblood	blood
30	chr19:40333200-40335600	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr19:40333200-40335800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr19:40333200-40335800	Enhancers	Colon Smooth Muscle	Colon
33	chr19:40333200-40335800	Flanking Active TSS	GM12878-XiMat	blood
34	chr19:40333200-40336000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr19:40333200-40336200	Flanking Active TSS	Dnd41	blood
36	chr19:40333400-40335200	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr19:40333400-40335200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr19:40333400-40335200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr19:40333400-40335200	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr19:40333400-40335600	Enhancers	Pancreas	Pancrea
41	chr19:40333400-40335800	Enhancers	Fetal Muscle Leg	muscle
42	chr19:40333400-40335800	Enhancers	Ovary	ovary
43	chr19:40333400-40336000	Enhancers	Primary B cells from peripheral blood	blood
44	chr19:40333400-40336000	Enhancers	Left Ventricle	heart
45	chr19:40333400-40336600	Enhancers	Spleen	Spleen
46	chr19:40333600-40335200	Enhancers	NHDF-Ad	bronchial
47	chr19:40333600-40335200	Enhancers	NHLF	lung
48	chr19:40333600-40335400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:40333600-40336200	Weak transcription	Aorta	Aorta
50	chr19:40333800-40335200	Enhancers	HUVEC	blood vessel

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