Variant report

Variant	rs9964099
Chromosome Location	chr18:12653673-12653674
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	GATA3	chr18:12652756-12653720	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr18:12652706-12653772	SK-N-SH	brain:	n/a	n/a
3	PBX3	chr18:12652892-12653699	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr18:12652880-12653759	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr18:12652707-12653819	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:12648702..12654959-chr18:12655130..12658770,8	K562	blood:
2	chr18:12643422..12646156-chr18:12653146..12655533,3	MCF-7	breast:
3	chr18:12649857..12654959-chr18:12655130..12658770,11	K562	blood:
4	chr18:12651259..12653780-chr18:12656567..12658681,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215527	TF binding region
SPIRE1	TF binding region
ENSG00000134278	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000128789	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs28666956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9949591	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9960169	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1820040	chr18:12635601-12725236	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh 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	20 gene(s)	inside rSNPs	diseases
7	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv1791969	chr18:12643193-12697711	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	esv3397790	chr18:12649001-12673755	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv576497	chr18:12650900-12658293	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	nsv576498	chr18:12650900-12658436	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12633600-12655800	Weak transcription	Fetal Stomach	stomach
2	chr18:12646000-12654000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr18:12646200-12657000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr18:12646200-12657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr18:12646400-12656600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr18:12646400-12656600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr18:12646400-12657000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr18:12648000-12656800	Weak transcription	Left Ventricle	heart
9	chr18:12648400-12656600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr18:12648600-12655800	Weak transcription	Fetal Muscle Leg	muscle
11	chr18:12648600-12656800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr18:12650000-12654400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr18:12651000-12654000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr18:12651400-12653800	Enhancers	Brain Cingulate Gyrus	brain
15	chr18:12651800-12654000	Enhancers	Brain Hippocampus Middle	brain
16	chr18:12652200-12655400	Enhancers	Fetal Brain Male	brain
17	chr18:12652400-12654000	Enhancers	Adipose Nuclei	Adipose
18	chr18:12652400-12654000	Enhancers	HUVEC	blood vessel
19	chr18:12652600-12654000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr18:12652600-12655400	Weak transcription	Fetal Kidney	kidney
21	chr18:12652800-12653800	Enhancers	Ovary	ovary
22	chr18:12652800-12653800	Enhancers	K562	blood
23	chr18:12652800-12654200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr18:12653000-12653800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr18:12653000-12653800	Enhancers	Dnd41	blood
26	chr18:12653000-12653800	Enhancers	HepG2	liver
27	chr18:12653000-12653800	Enhancers	NHLF	lung
28	chr18:12653000-12654000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr18:12653000-12655800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr18:12653200-12653800	Enhancers	Hela-S3	cervix
31	chr18:12653200-12653800	Enhancers	Osteobl	bone
32	chr18:12653200-12656400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr18:12653200-12656600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr18:12653200-12656600	Weak transcription	Right Atrium	heart
35	chr18:12653200-12656600	Weak transcription	Right Ventricle	heart
36	chr18:12653200-12656800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr18:12653200-12656800	Weak transcription	Esophagus	oesophagus
38	chr18:12653200-12657000	Weak transcription	Spleen	Spleen
39	chr18:12653400-12653800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr18:12653400-12654000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr18:12653400-12654000	Enhancers	Muscle Satellite Cultured Cells	--
42	chr18:12653400-12654000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr18:12653400-12654200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr18:12653400-12655000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr18:12653400-12655000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr18:12653400-12655400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr18:12653400-12655400	Weak transcription	NHEK	skin
48	chr18:12653400-12655600	Weak transcription	HMEC	breast
49	chr18:12653400-12656400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr18:12653400-12656400	Weak transcription	Stomach Smooth Muscle	stomach

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