Variant report

Variant	rs1879307
Chromosome Location	chr10:43757943-43757944
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43716710..43720339-chr10:43755141..43758566,3	K562	blood:
2	chr10:43746978..43749423-chr10:43756169..43758679,2	K562	blood:
3	chr10:43749564..43751225-chr10:43756675..43758831,2	K562	blood:
4	chr10:43757038..43760449-chr10:43762640..43764974,3	K562	blood:
5	chr10:43745055..43746859-chr10:43757087..43758973,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10899787	1.00[YRI][hapmap]
rs1879301	1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1879303	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1879305	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1879316	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2253524	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2253527	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2460557	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2503858	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2505526	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505549	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7090455	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7900769	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs868314	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv895083	chr10:43549708-43765485	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv1831010	chr10:43674916-43759185	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv895084	chr10:43688505-43765485	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS 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	nsv466881	chr10:43695049-43799588	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv550696	chr10:43695049-43799588	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv895085	chr10:43695049-43804617	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv825351	chr10:43714249-43788481	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1035873	chr10:43721143-43873664	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv466882	chr10:43721481-43849358	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv550697	chr10:43721481-43849358	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv895086	chr10:43731521-43767816	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv1044422	chr10:43731521-43860307	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	esv1846074	chr10:43744741-43761629	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1879307	CXCL12	cis	parietal	SCAN
rs1879307	CSGALNACT2	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43746200-43760000	Weak transcription	A549	lung
2	chr10:43750800-43761600	Weak transcription	Right Atrium	heart
3	chr10:43754600-43758000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
4	chr10:43756000-43760600	Weak transcription	Pancreas	Pancrea
5	chr10:43756800-43758000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr10:43756800-43758600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr10:43757000-43758200	Weak transcription	Fetal Brain Female	brain
8	chr10:43757200-43758000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr10:43757200-43758000	Enhancers	Brain Anterior Caudate	brain
10	chr10:43757200-43758400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:43757200-43760600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr10:43757200-43761000	Enhancers	Fetal Brain Male	brain
13	chr10:43757400-43758000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr10:43757400-43758000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr10:43757400-43758200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr10:43757400-43758200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
17	chr10:43757400-43759200	Weak transcription	Brain Angular Gyrus	brain
18	chr10:43757600-43758000	Enhancers	Brain Germinal Matrix	brain
19	chr10:43757600-43760400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr10:43757800-43758000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr10:43757800-43758000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain

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