Variant report

Variant	rs10485822
Chromosome Location	chr20:1246412-1246413
allele	C/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	chr20:1245990-1247009	SK-N-SH	brain:	n/a	n/a
2	ZC3H11A	chr20:1246151-1246825	K562	blood:	n/a	n/a
3	TBL1XR1	chr20:1245384-1246965	K562	blood:	n/a	n/a
4	RCOR1	chr20:1245602-1247705	K562	blood:	n/a	n/a
5	GATA2	chr20:1245996-1246815	SH-SY5Y	brain:	n/a	chr20:1246207-1246221
6	EP300	chr20:1245913-1246961	K562	blood:	n/a	n/a
7	JUND	chr20:1245882-1247729	K562	blood:	n/a	chr20:1247528-1247539 chr20:1247526-1247536 chr20:1247525-1247536
8	KAP1	chr20:1246373-1246848	U2OS	brain:	n/a	n/a
9	RCOR1	chr20:1246143-1248264	IMR90	lung:	n/a	n/a
10	GATA2	chr20:1246130-1246559	HUVEC	blood vessel:	n/a	chr20:1246207-1246221
11	MAX	chr20:1246373-1247276	HCT-116	colon:	n/a	chr20:1247218-1247228
12	MAFK	chr20:1246173-1246731	K562	blood:	n/a	n/a
13	ARID3A	chr20:1245941-1246879	K562	blood:	n/a	n/a
14	GATA3	chr20:1246256-1246567	SH-SY5Y	brain:	n/a	n/a
15	IRF1	chr20:1246169-1246974	K562	blood:	n/a	chr20:1246914-1246928
16	GATA3	chr20:1246047-1246735	SK-N-SH	brain:	n/a	n/a
17	JUN	chr20:1246400-1246792	H1-hESC	embryonic stem cell:	n/a	n/a
18	RCOR1	chr20:1245618-1246844	K562	blood:	n/a	n/a
19	REST	chr20:1246403-1248350	H1-neurons	neurons:	n/a	chr20:1247428-1247441 chr20:1247424-1247434 chr20:1247092-1247112 chr20:1247419-1247432
20	MAX	chr20:1246376-1247748	A549	lung:	n/a	chr20:1247585-1247595 chr20:1247218-1247228 chr20:1247527-1247536

No.	Distal block	Cell Line	Cell type
1	chr20:1204614..1208313-chr20:1245857..1250887,4	K562	blood:
2	chr20:1206512..1208051-chr20:1245857..1247433,2	K562	blood:
3	chr20:633104..634998-chr20:1246105..1248133,2	K562	blood:

Variant related genes	Relation type
SNPH	TF binding region
ENSG00000244588	Chromatin interaction
ENSG00000271303	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1407766	1.00[CHB][hapmap]
rs17717241	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17779421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813073	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814030	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814031	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040984	0.89[ASN][1000 genomes]
rs60609218	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7265362	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs7273889	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs73890804	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73890806	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73890814	0.82[AFR][1000 genomes]
rs8122738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058524	chr20:821434-1254865	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription 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	23 gene(s)	inside rSNPs	diseases
2	nsv544138	chr20:821434-1254865	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh 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 miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1057939	chr20:824980-1316778	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS 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	34 gene(s)	inside rSNPs	diseases
4	nsv1057097	chr20:1030940-1314265	Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv912586	chr20:1195784-1248286	Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv518957	chr20:1195784-1250463	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv912587	chr20:1205886-1248286	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv1816838	chr20:1230185-1247015	Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv1067360	chr20:1245753-1283508	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1244600-1246600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:1245000-1246600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:1245000-1246600	Weak transcription	Placenta	Placenta
4	chr20:1245400-1246800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
5	chr20:1245400-1246800	Flanking Active TSS	K562	blood
6	chr20:1245600-1246600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr20:1245800-1246600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr20:1245800-1246800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr20:1246000-1246600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr20:1246000-1246600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr20:1246000-1246600	Enhancers	Primary hematopoietic stem cells	blood
12	chr20:1246000-1246600	Enhancers	Esophagus	oesophagus
13	chr20:1246000-1246600	Enhancers	Gastric	stomach
14	chr20:1246000-1246800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr20:1246000-1246800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr20:1246000-1246800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr20:1246000-1247600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr20:1246200-1246600	Enhancers	H9 Cell Line	embryonic stem cell
19	chr20:1246200-1246600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr20:1246200-1246600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr20:1246200-1246600	Enhancers	Primary B cells from peripheral blood	blood
22	chr20:1246200-1246600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr20:1246200-1246600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr20:1246200-1246600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr20:1246200-1246600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr20:1246200-1246600	Enhancers	Colonic Mucosa	Colon
27	chr20:1246200-1246600	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr20:1246200-1246600	Flanking Active TSS	A549	lung
29	chr20:1246200-1246600	Enhancers	HUVEC	blood vessel
30	chr20:1246200-1246800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr20:1246200-1246800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr20:1246200-1246800	Flanking Active TSS	Stomach Mucosa	stomach
33	chr20:1246200-1247800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr20:1246200-1248200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr20:1246400-1246600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr20:1246400-1246600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr20:1246400-1246600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr20:1246400-1246600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
39	chr20:1246400-1246600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr20:1246400-1246600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
41	chr20:1246400-1246600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr20:1246400-1246600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
43	chr20:1246400-1246600	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr20:1246400-1246600	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr20:1246400-1246600	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr20:1246400-1246600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr20:1246400-1246600	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr20:1246400-1246600	Enhancers	Colon Smooth Muscle	Colon
49	chr20:1246400-1246600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr20:1246400-1246600	Flanking Active TSS	Fetal Brain Male	brain

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