Variant report

Variant	rs2943672
Chromosome Location	chr1:85106040-85106041
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	POLR2A	chr1:85105538-85106845	K562	blood:	n/a	n/a
2	POLR2A	chr1:85105441-85106246	K562	blood:	n/a	n/a
3	GATA1	chr1:85105507-85106062	K562	blood:	n/a	n/a
4	BHLHE40	chr1:85106034-85106138	K562	blood:	n/a	n/a
5	CCNT2	chr1:85105533-85106223	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:85097469..85099752-chr1:85104402..85106141,3	K562	blood:
2	chr1:85097617..85099752-chr1:85104545..85106141,2	K562	blood:
3	chr1:85105975..85107759-chr1:85109994..85111920,2	K562	blood:

Variant related genes	Relation type
ENSG00000232622	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11578078	0.85[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap]
rs12022113	0.85[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap]
rs12120614	0.88[EUR][1000 genomes]
rs12123923	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12125951	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12127432	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1340527	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1340528	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2298076	1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2911567	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2911571	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2911575	0.81[ASN][1000 genomes]
rs2911578	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2911611	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]
rs2994429	0.93[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2994437	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs2994439	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2994440	0.88[ASN][1000 genomes]
rs2994449	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2994941	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2994949	1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3096445	0.92[CHB][hapmap];0.94[CHD][hapmap];0.86[ASN][1000 genomes]
rs3768238	0.92[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs3782	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs4390189	0.81[ASN][1000 genomes]
rs4551615	0.81[ASN][1000 genomes]
rs56681543	0.81[ASN][1000 genomes]
rs6576722	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs6576723	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs6670415	0.82[ASN][1000 genomes]
rs6682889	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6687220	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7545555	0.83[ASN][1000 genomes]
rs9661716	0.92[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2943672	LMO4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85087000-85147400	Weak transcription	Gastric	stomach
2	chr1:85099000-85109600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:85099000-85115600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:85099000-85123400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:85099200-85109200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:85099200-85109800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:85099200-85115000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:85099200-85121400	Weak transcription	NHDF-Ad	bronchial
9	chr1:85099200-85138200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:85099400-85115000	Weak transcription	Osteobl	bone
11	chr1:85099400-85131200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:85099600-85122600	Weak transcription	Fetal Brain Male	brain
13	chr1:85100200-85106200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:85100600-85112400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:85100600-85116800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:85101000-85123200	Weak transcription	Fetal Kidney	kidney
17	chr1:85101000-85124400	Weak transcription	Hela-S3	cervix
18	chr1:85101400-85109000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:85101600-85121000	Weak transcription	Placenta	Placenta
20	chr1:85103000-85115000	Weak transcription	HMEC	breast
21	chr1:85104600-85116000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:85104800-85111600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:85105000-85119000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:85105600-85106200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:85105600-85106200	Enhancers	K562	blood
26	chr1:85105600-85106200	Enhancers	NHEK	skin
27	chr1:85105800-85106200	Enhancers	Fetal Intestine Large	intestine
28	chr1:85105800-85106600	Enhancers	Duodenum Mucosa	Duodenum
29	chr1:85105800-85106800	Enhancers	Fetal Intestine Small	intestine
30	chr1:85105800-85115000	Weak transcription	Small Intestine	intestine
31	chr1:85106000-85106200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:85106000-85106200	Enhancers	Fetal Heart	heart
33	chr1:85106000-85110800	Weak transcription	Fetal Thymus	thymus
34	chr1:85106000-85116600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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