Variant report

Variant	rs2631716
Chromosome Location	chr15:40070017-40070018
allele	A/C
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	FOXA1	chr15:40069960-40070415	HepG2	liver:	n/a	chr15:40070158-40070173
2	FOSL2	chr15:40069909-40070210	HepG2	liver:	n/a	chr15:40070059-40070068 chr15:40070059-40070066 chr15:40070059-40070067 chr15:40070058-40070067
3	FOXA1	chr15:40069990-40070306	HepG2	liver:	n/a	chr15:40070158-40070173
4	FOXA2	chr15:40069980-40070296	HepG2	liver:	n/a	n/a
5	FOXA1	chr15:40069989-40070256	HepG2	liver:	n/a	chr15:40070158-40070173
6	BATF	chr15:40069632-40070061	GM12878	blood:	n/a	n/a
7	JUND	chr15:40069926-40070179	HepG2	liver:	n/a	chr15:40070059-40070068 chr15:40070059-40070066 chr15:40070059-40070067 chr15:40070058-40070067 chr15:40070057-40070068
8	FOXA1	chr15:40069846-40070319	HepG2	liver:	n/a	chr15:40070158-40070173

No.	Distal block	Cell Line	Cell type
1	chr15:39979023..39981258-chr15:40069325..40071839,2	K562	blood:
2	chr15:40058706..40061655-chr15:40069031..40071989,2	MCF-7	breast:
3	chr15:40069274..40072171-chr15:40072532..40074529,2	MCF-7	breast:
4	chr15:40068522..40070743-chr15:40450771..40453010,2	K562	blood:

Variant related genes	Relation type
ENSG00000261136	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1027230	1.00[AFR][1000 genomes]
rs1027231	1.00[AFR][1000 genomes]
rs1166719	1.00[AFR][1000 genomes]
rs1166720	1.00[AFR][1000 genomes]
rs1166726	0.95[AFR][1000 genomes]
rs1688088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2631691	1.00[AFR][1000 genomes]
rs2631719	1.00[AFR][1000 genomes]
rs2638008	1.00[AFR][1000 genomes]
rs2638011	1.00[AFR][1000 genomes]
rs589137	0.95[AFR][1000 genomes]
rs596717	1.00[AFR][1000 genomes]
rs603993	0.95[AFR][1000 genomes]
rs612775	1.00[AFR][1000 genomes]
rs621970	0.81[AFR][1000 genomes]
rs623984	1.00[AFR][1000 genomes]
rs628076	1.00[AFR][1000 genomes]
rs653964	0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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	17 gene(s)	inside rSNPs	diseases
2	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40059400-40074400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:40063800-40074000	Weak transcription	Brain Angular Gyrus	brain
3	chr15:40064000-40074000	Weak transcription	Brain Anterior Caudate	brain
4	chr15:40064200-40073800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:40064400-40074200	Weak transcription	Osteobl	bone
6	chr15:40066800-40070800	Enhancers	Primary hematopoietic stem cells	blood
7	chr15:40067400-40071600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:40067400-40071800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr15:40067600-40073800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr15:40068000-40073800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr15:40068200-40073800	Weak transcription	Dnd41	blood
12	chr15:40068800-40070600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr15:40068800-40070800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr15:40069400-40070200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:40069400-40070200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr15:40069400-40070200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:40069400-40070400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr15:40069400-40070400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:40069400-40070400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:40069400-40070400	Enhancers	HepG2	liver
21	chr15:40069400-40070600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:40069400-40070600	Enhancers	Fetal Stomach	stomach
23	chr15:40069400-40070600	Enhancers	K562	blood
24	chr15:40069400-40070800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:40069600-40070200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:40069600-40070200	Enhancers	HSMMtube	muscle
27	chr15:40069600-40070400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr15:40069600-40070400	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr15:40069600-40070400	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr15:40069600-40070400	Enhancers	NH-A	brain
31	chr15:40069600-40070600	Enhancers	H1 Cell Line	embryonic stem cell
32	chr15:40069600-40070800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr15:40069800-40070200	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr15:40069800-40070200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:40069800-40070400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:40069800-40070400	Enhancers	Fetal Kidney	kidney
37	chr15:40069800-40070600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr15:40069800-40070800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:40069800-40074000	Weak transcription	GM12878-XiMat	blood
40	chr15:40070000-40070200	Enhancers	Fetal Muscle Leg	muscle
41	chr15:40070000-40070400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:40070000-40071600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr15:40070000-40074200	Weak transcription	NHDF-Ad	bronchial

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