Variant report

Variant	rs2412772
Chromosome Location	chr4:57838999-57839000
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	KAP1	chr4:57838868-57839531	K562	blood:	n/a	n/a
2	SETDB1	chr4:57838865-57839480	U2OS	brain:	n/a	n/a
3	CBX3	chr4:57838998-57839367	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57822641..57828782-chr4:57838494..57846737,10	K562	blood:
2	chr4:57832993..57836325-chr4:57837117..57839570,3	K562	blood:
3	chr4:57832384..57834493-chr4:57837035..57839570,2	K562	blood:

Variant related genes	Relation type
POLR2B	TF binding region
ENSG00000269949	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10030913	0.80[EUR][1000 genomes]
rs10866440	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs10866441	0.96[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs1105434	0.96[CEU][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs11133472	0.93[TSI][hapmap]
rs11133474	0.93[TSI][hapmap]
rs11736869	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs11736965	0.83[EUR][1000 genomes]
rs11737689	0.90[EUR][1000 genomes]
rs12500454	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs12501224	0.91[EUR][1000 genomes]
rs12501990	0.88[EUR][1000 genomes]
rs12502076	0.91[EUR][1000 genomes]
rs1277284	1.00[JPT][hapmap]
rs13108245	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs13113802	0.81[EUR][1000 genomes]
rs13119525	0.90[EUR][1000 genomes]
rs13131605	0.82[EUR][1000 genomes]
rs13136432	0.91[EUR][1000 genomes]
rs13150593	0.91[EUR][1000 genomes]
rs13152476	0.86[EUR][1000 genomes]
rs1713997	1.00[JPT][hapmap]
rs1718882	1.00[JPT][hapmap]
rs1718886	1.00[JPT][hapmap]
rs1877669	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs1963666	0.89[EUR][1000 genomes]
rs2014870	0.90[EUR][1000 genomes]
rs3000	0.96[CEU][hapmap];0.92[TSI][hapmap]
rs34124552	0.91[EUR][1000 genomes]
rs34448457	0.91[EUR][1000 genomes]
rs35267092	0.91[EUR][1000 genomes]
rs3796531	0.95[JPT][hapmap]
rs4339274	0.80[GIH][hapmap]
rs4864608	0.89[EUR][1000 genomes]
rs4865172	0.92[CEU][hapmap]
rs62308155	0.90[EUR][1000 genomes]
rs6554398	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6838948	0.96[CEU][hapmap];0.90[TSI][hapmap]
rs6852110	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7668814	0.95[JPT][hapmap]
rs7680734	0.96[CEU][hapmap];0.92[TSI][hapmap];0.89[EUR][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	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2412772	TXNDC9	cis	parietal	SCAN
rs2412772	KIAA1211	cis	parietal	SCAN
rs2412772	IGFBP7	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57793600-57842000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:57793600-57842000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:57826400-57839800	Strong transcription	Primary T cells from cord blood	blood
4	chr4:57826600-57839000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:57826600-57839200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:57826600-57840800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:57826600-57840800	Strong transcription	Fetal Brain Female	brain
8	chr4:57826600-57840800	Strong transcription	Fetal Muscle Leg	muscle
9	chr4:57826600-57840800	Strong transcription	Fetal Thymus	thymus
10	chr4:57826600-57841000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:57826600-57841400	Strong transcription	Fetal Intestine Large	intestine
12	chr4:57826800-57839000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:57826800-57840800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:57826800-57840800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:57826800-57840800	Weak transcription	Stomach Mucosa	stomach
16	chr4:57827000-57840400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:57827000-57843200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr4:57827200-57839000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:57827200-57840200	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr4:57827200-57840400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:57827200-57840400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr4:57827200-57840600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:57827200-57840800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr4:57827200-57840800	Strong transcription	Dnd41	blood
25	chr4:57827200-57841000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:57827200-57841000	Strong transcription	Fetal Lung	lung
27	chr4:57827200-57841400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:57827400-57839600	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr4:57827400-57839600	Strong transcription	Placenta	Placenta
30	chr4:57827400-57841000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr4:57827600-57840200	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:57827600-57840600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr4:57827800-57839200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:57827800-57839200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:57828000-57840400	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr4:57828000-57840600	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr4:57828200-57840200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr4:57828200-57840400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr4:57828200-57841200	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr4:57828400-57839000	Strong transcription	Brain Germinal Matrix	brain
41	chr4:57828400-57839200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr4:57828400-57839200	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr4:57828800-57840400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:57829400-57840400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:57830600-57839400	Strong transcription	K562	blood
46	chr4:57830600-57840200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
47	chr4:57832200-57840200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:57833000-57839000	Weak transcription	Fetal Brain Male	brain
49	chr4:57834600-57841000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr4:57835000-57840200	Strong transcription	Brain Hippocampus Middle	brain

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