Variant report

Variant	rs12004510
Chromosome Location	chr9:98636080-98636081
allele	C/T
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	MAFK	chr9:98635899-98636172	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98531848..98533634-chr9:98635544..98637181,2	MCF-7	breast:
2	chr9:98614433..98624477-chr9:98629889..98639636,23	MCF-7	breast:

Variant related genes	Relation type
ERCC6L2	TF binding region
ENSG00000252847	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11998816	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12000947	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12001253	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12004765	0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45604033	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55870020	1.00[EUR][1000 genomes]
rs56275194	1.00[EUR][1000 genomes]
rs56938111	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58715455	1.00[EUR][1000 genomes]
rs59510923	1.00[EUR][1000 genomes]
rs60301271	1.00[EUR][1000 genomes]
rs6478983	1.00[EUR][1000 genomes]
rs6479043	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7021641	1.00[EUR][1000 genomes]
rs7030110	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7030427	1.00[EUR][1000 genomes]
rs7031397	1.00[EUR][1000 genomes]
rs7039115	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7041571	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7043426	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7043732	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7046189	1.00[EUR][1000 genomes]
rs7047126	1.00[EUR][1000 genomes]
rs73528896	1.00[EUR][1000 genomes]
rs73528901	1.00[EUR][1000 genomes]
rs73530711	1.00[EUR][1000 genomes]
rs73534614	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73656542	1.00[EUR][1000 genomes]
rs73656543	1.00[EUR][1000 genomes]
rs73656554	1.00[EUR][1000 genomes]
rs73656561	1.00[EUR][1000 genomes]
rs73656564	1.00[EUR][1000 genomes]
rs7847478	1.00[EUR][1000 genomes]
rs7850319	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7854738	1.00[EUR][1000 genomes]
rs7860019	1.00[EUR][1000 genomes]
rs7875882	1.00[EUR][1000 genomes]
rs892647	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98610200-98636200	Weak transcription	Brain Germinal Matrix	brain
2	chr9:98610200-98636800	Weak transcription	Gastric	stomach
3	chr9:98620400-98636200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:98620600-98636600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:98621000-98636400	Weak transcription	Hela-S3	cervix
6	chr9:98624600-98636400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:98625000-98636200	Weak transcription	Fetal Lung	lung
8	chr9:98626200-98636400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:98628000-98636400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:98628200-98636200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr9:98628400-98636800	Weak transcription	Thymus	Thymus
12	chr9:98629200-98636600	Weak transcription	Primary B cells from cord blood	blood
13	chr9:98630200-98636200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr9:98630400-98636600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:98630600-98636200	Weak transcription	Brain Anterior Caudate	brain
16	chr9:98630600-98636400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:98631200-98636600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr9:98631200-98636600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr9:98631200-98636600	Weak transcription	NH-A	brain
20	chr9:98631400-98636400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:98631400-98636600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr9:98631400-98636600	Weak transcription	Osteobl	bone
23	chr9:98631800-98636400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:98631800-98636400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr9:98631800-98636800	Weak transcription	Ovary	ovary
26	chr9:98632000-98636800	Weak transcription	Esophagus	oesophagus
27	chr9:98632200-98636400	Weak transcription	Fetal Intestine Small	intestine
28	chr9:98632200-98636600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr9:98632400-98636800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr9:98632600-98636600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:98632800-98636400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:98632800-98636800	Weak transcription	Placenta	Placenta
33	chr9:98632800-98636800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:98633000-98636600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:98633000-98636800	Weak transcription	HSMMtube	muscle
36	chr9:98633200-98636200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr9:98633200-98636400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr9:98633200-98636400	Weak transcription	HMEC	breast
39	chr9:98633200-98636600	Weak transcription	Adipose Nuclei	Adipose
40	chr9:98633200-98636800	Weak transcription	Fetal Thymus	thymus
41	chr9:98633400-98636400	Weak transcription	Colonic Mucosa	Colon
42	chr9:98633400-98636400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr9:98633400-98636600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr9:98633400-98636600	Weak transcription	Brain Angular Gyrus	brain
45	chr9:98633400-98636600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr9:98633400-98636600	Weak transcription	Fetal Brain Male	brain
47	chr9:98633600-98636400	Weak transcription	A549	lung
48	chr9:98633600-98636800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr9:98633800-98636200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr9:98633800-98636400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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