Variant report

Variant	rs10842928
Chromosome Location	chr12:9285974-9285975
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	chr12:9285745-9286318	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr12:9285626-9286468	SK-N-SH	brain:	n/a	chr12:9285731-9285739
3	MAX	chr12:9285814-9286437	Hela-S3	cervix:	n/a	n/a
4	TCF7L2	chr12:9285753-9286449	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr12:9285768-9286913	Hela-S3	cervix:	n/a	n/a
6	PBX3	chr12:9285727-9286145	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr12:9285789-9286196	MCF-7	breast:	n/a	n/a
8	JUND	chr12:9285750-9286182	SK-N-SH	brain:	n/a	n/a
9	TCF12	chr12:9285744-9286281	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr12:9285639-9286308	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000256720	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10771357	0.94[CEU][hapmap]
rs10842914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10842923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842970	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10842971	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11513245	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12820449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822596	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12823677	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2114851	0.88[CEU][hapmap]
rs226369	0.89[CEU][hapmap]
rs226370	0.89[CEU][hapmap]
rs226372	0.94[CEU][hapmap]
rs2303615	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2377740	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3759276	0.88[CEU][hapmap]
rs4367994	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4883215	0.86[YRI][hapmap]
rs7305636	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309811	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7309821	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7953026	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7959552	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967599	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7968546	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7968679	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7978666	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	esv3504674	chr12:9243858-9318016	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv3502154	chr12:9243906-9317851	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3502155	chr12:9243906-9317851	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3504685	chr12:9243948-9317959	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv527404	chr12:9250601-9435244	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
8	nsv976735	chr12:9274937-9303290	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9262800-9289000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:9269000-9319200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:9270200-9289000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:9272000-9289000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:9275000-9287400	Weak transcription	Gastric	stomach
6	chr12:9277600-9288800	Weak transcription	Right Atrium	heart
7	chr12:9280800-9310400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:9281000-9288400	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr12:9281200-9287600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:9281400-9289800	Weak transcription	Primary T cells from cord blood	blood
11	chr12:9282600-9287800	Enhancers	HepG2	liver
12	chr12:9284400-9286800	Enhancers	Fetal Intestine Small	intestine
13	chr12:9284400-9287000	Enhancers	Fetal Intestine Large	intestine
14	chr12:9284400-9289000	Enhancers	Fetal Lung	lung
15	chr12:9284600-9286400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:9284600-9287000	Enhancers	Hela-S3	cervix
17	chr12:9285000-9287400	Enhancers	Fetal Stomach	stomach
18	chr12:9285200-9286800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:9285400-9286400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:9285600-9286000	Flanking Active TSS	Liver	Liver
21	chr12:9285600-9286000	Weak transcription	HMEC	breast
22	chr12:9285600-9286000	Weak transcription	NHLF	lung
23	chr12:9285600-9287600	Weak transcription	Pancreas	Pancrea

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