Variant report

Variant	rs12296371
Chromosome Location	chr12:21589848-21589849
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	HCFC1	chr12:21588964-21591600	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:21569338..21572113-chr12:21589171..21592854,4	K562	blood:
2	chr12:21569338..21572113-chr12:21589171..21592483,4	K562	blood:
3	chr12:21589456..21592020-chr12:21808889..21812230,4	K562	blood:

Variant related genes	Relation type
PYROXD1	TF binding region
ENSG00000084453	Chromatin interaction
ENSG00000111716	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11046062	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12296109	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12297304	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12297936	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12309454	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12311412	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12315190	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7315988	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526789	chr12:21555691-21590788	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	nsv898895	chr12:21561645-21621891	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv469163	chr12:21579080-21592357	Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
7	nsv557742	chr12:21579080-21592357	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21581800-21590000	Weak transcription	HUVEC	blood vessel
2	chr12:21587200-21590200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:21589400-21590000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:21589400-21590200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:21589800-21590000	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr12:21589800-21590000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr12:21589800-21590000	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr12:21589800-21590000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:21589800-21590000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr12:21589800-21590000	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr12:21589800-21590000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:21589800-21590000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr12:21589800-21590000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:21589800-21590000	Active TSS	Brain Cingulate Gyrus	brain
15	chr12:21589800-21590000	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr12:21589800-21590000	Active TSS	Duodenum Mucosa	Duodenum
17	chr12:21589800-21590000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr12:21589800-21590000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr12:21589800-21590000	Enhancers	Rectal Smooth Muscle	rectum
20	chr12:21589800-21590000	Enhancers	A549	lung
21	chr12:21589800-21590000	Enhancers	Dnd41	blood
22	chr12:21589800-21590200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:21589800-21590200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:21589800-21590200	Flanking Active TSS	Hela-S3	cervix
25	chr12:21589800-21590200	Flanking Active TSS	HMEC	breast
26	chr12:21589800-21590200	Flanking Active TSS	K562	blood
27	chr12:21589800-21590200	Flanking Active TSS	Osteobl	bone
28	chr12:21589800-21590400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:21589800-21591400	Active TSS	Fetal Kidney	kidney
30	chr12:21589800-21591600	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr12:21589800-21591600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:21589800-21591600	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr12:21589800-21591600	Active TSS	HSMMtube	muscle
34	chr12:21589800-21592000	Active TSS	Rectal Mucosa Donor 29	rectum

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