Variant report

Variant	rs12223401
Chromosome Location	chr11:58985080-58985081
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	RUNX3	chr11:58983838-58985112	GM12878	blood:	n/a	n/a
2	PML	chr11:58983861-58985185	GM12878	blood:	n/a	n/a
3	IKZF1	chr11:58983887-58985123	GM12878	blood:	n/a	n/a
4	RUNX3	chr11:58983839-58985157	GM12878	blood:	n/a	n/a
5	NFATC1	chr11:58983856-58985142	GM12878	blood:	n/a	n/a
6	MTA3	chr11:58983751-58985251	GM12878	blood:	n/a	n/a
7	NFIC	chr11:58983826-58985160	GM12878	blood:	n/a	n/a
8	SPI1	chr11:58983561-58985173	GM12878	blood:	n/a	chr11:58984226-58984239 chr11:58985085-58985092 chr11:58984228-58984237 chr11:58984449-58984458 chr11:58984225-58984238 chr11:58984610-58984623

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58985014..58986524-chr11:58989804..58992131,2	K562	blood:

Variant related genes	Relation type
RN7SL42P	TF binding region
MPEG1	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1048696	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10501375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10501376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10896957	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11229868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229872	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11229873	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11229874	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11229875	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11229882	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11229889	0.88[CEU][hapmap]
rs11229901	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11229902	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11229903	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11229904	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12575770	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12576150	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12576412	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12576558	0.87[EUR][1000 genomes]
rs12576879	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12577252	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17153538	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35654554	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3740946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3781796	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59466005	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60265864	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61086875	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7104296	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7104437	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7926933	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7942203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs869155	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv3351601	chr11:58979308-59052763	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12223401	DTX4	Cis_1M	lymphoblastoid	RTeQTL
rs12223401	MPEG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58975400-58986600	Weak transcription	Gastric	stomach
2	chr11:58976000-58989400	Weak transcription	Stomach Mucosa	stomach
3	chr11:58979200-58989600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:58979800-58985200	Weak transcription	Pancreas	Pancrea
5	chr11:58980400-58991200	Weak transcription	Fetal Muscle Leg	muscle
6	chr11:58981000-58991600	Weak transcription	Spleen	Spleen
7	chr11:58982800-58986000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr11:58983000-58985200	Enhancers	Primary hematopoietic stem cells	blood
9	chr11:58983600-58985200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr11:58983800-58985400	Enhancers	Fetal Stomach	stomach
11	chr11:58984000-58985200	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr11:58984000-58985200	Enhancers	Fetal Kidney	kidney
13	chr11:58984000-58985200	Enhancers	Fetal Lung	lung
14	chr11:58984000-58985800	Enhancers	Adipose Nuclei	Adipose
15	chr11:58984200-58985200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr11:58984200-58988200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:58984400-58986200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr11:58984400-58990600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr11:58984600-58985200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr11:58984600-58985800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr11:58984600-58988400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr11:58984600-58990600	Weak transcription	Placenta	Placenta
23	chr11:58984600-58990600	Weak transcription	Fetal Thymus	thymus
24	chr11:58984800-58985400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:58984800-58986000	Enhancers	NHDF-Ad	bronchial
26	chr11:58984800-58987200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr11:58984800-58988200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr11:58984800-58988200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr11:58984800-58988200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr11:58984800-58988600	Weak transcription	Hela-S3	cervix
31	chr11:58985000-58985200	Enhancers	Rectal Smooth Muscle	rectum
32	chr11:58985000-58985400	Weak transcription	NHLF	lung
33	chr11:58985000-58985600	Enhancers	GM12878-XiMat	blood
34	chr11:58985000-58987200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:58985000-58988600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr11:58985000-58988600	Weak transcription	Colon Smooth Muscle	Colon
37	chr11:58985000-58989600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr11:58985000-58990600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:58985000-58991600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr11:58985000-58993200	Enhancers	Primary B cells from peripheral blood	blood

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