Variant report

Variant	rs3025388
Chromosome Location	chr9:136503256-136503257
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:136475965..136477693-chr9:136502084..136503686,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1108580	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs1108581	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13284520	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1548364	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs1548367	0.91[ASN][1000 genomes]
rs1611120	0.82[JPT][hapmap]
rs1611122	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs1611123	0.82[JPT][hapmap]
rs1611125	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs2519151	0.86[ASN][1000 genomes]
rs2519156	0.99[ASN][1000 genomes]
rs2873804	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs3025383	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3025385	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3025386	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5320	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894077	chr9:136166346-136515297	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv894081	chr9:136227260-136678954	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS 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	43 gene(s)	inside rSNPs	diseases
3	nsv894086	chr9:136281753-136657960	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv894094	chr9:136311679-136528721	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv530972	chr9:136324358-136643044	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv894100	chr9:136371224-136547602	Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv870051	chr9:136459745-136656889	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv894105	chr9:136479571-136518097	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv982600	chr9:136488979-136503321	Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv894106	chr9:136489539-136566959	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong 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
11	nsv469906	chr9:136494566-136509083	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv894107	chr9:136494566-136579589	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv466615	chr9:136498143-136505241	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv615638	chr9:136498143-136505241	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv933084	chr9:136501384-136505120	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3025388	ITGAM	trans	lymphoblastoid	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136501600-136504200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:136501600-136505000	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
3	chr9:136501800-136507600	Weak transcription	Spleen	Spleen
4	chr9:136502400-136503800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr9:136502400-136503800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:136502400-136503800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:136502600-136503400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:136502600-136504000	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr9:136502600-136504200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:136502600-136504400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr9:136502800-136503400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:136502800-136503400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr9:136502800-136503400	Enhancers	Fetal Lung	lung
14	chr9:136502800-136503600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr9:136502800-136503600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr9:136502800-136503800	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr9:136503000-136503400	Enhancers	Fetal Kidney	kidney
18	chr9:136503000-136503600	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr9:136503200-136503400	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr9:136503200-136503600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr9:136503200-136503600	Enhancers	Fetal Thymus	thymus
22	chr9:136503200-136504600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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