Variant report

Variant	rs10930502
Chromosome Location	chr2:172890588-172890589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172889595..172892508-chr2:172896420..172898140,2	K562	blood:
2	chr2:172889910..172891414-chr2:172938513..172941287,2	MCF-7	breast:
3	chr2:172885240..172888005-chr2:172889269..172891539,4	MCF-7	breast:
4	chr2:172888478..172891307-chr2:172961439..172963560,3	K562	blood:
5	chr2:172885365..172888930-chr2:172890140..172893959,4	K562	blood:

Variant related genes	Relation type
ENSG00000172878	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10174055	0.87[CEU][hapmap]
rs10201053	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10202823	0.87[CEU][hapmap]
rs3770445	0.87[CEU][hapmap]
rs4668414	0.91[CEU][hapmap]
rs6433319	0.87[CEU][hapmap]
rs6715929	0.92[CEU][hapmap]
rs6724337	0.91[CEU][hapmap]
rs6725388	0.80[CEU][hapmap]
rs6727017	0.83[CEU][hapmap]
rs6731562	0.86[CEU][hapmap]
rs7573003	0.84[CEU][hapmap]
rs7594711	0.86[EUR][1000 genomes]
rs7606918	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10930502	AC068039.4	cis	Muscle Skeletal	GTEx
rs10930502	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs10930502	AC068039.4	cis	Esophagus Muscularis	GTEx
rs10930502	AC068039.4	cis	Whole Blood	GTEx
rs10930502	AC068039.4	cis	Thyroid	GTEx
rs10930502	AC068039.4	cis	Esophagus Mucosa	GTEx
rs10930502	AC068039.4	cis	Stomach	GTEx
rs10930502	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs10930502	AC068039.4	cis	lung	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172865600-172897400	Weak transcription	Primary T cells from cord blood	blood
2	chr2:172878600-172898200	Weak transcription	Primary B cells from cord blood	blood
3	chr2:172886800-172892800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:172887000-172893200	Weak transcription	Fetal Heart	heart
5	chr2:172887200-172892600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:172887200-172892600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:172887200-172892600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:172887200-172892800	Weak transcription	Brain Germinal Matrix	brain
9	chr2:172887200-172894000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:172887200-172894600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:172887200-172896600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:172887400-172892600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:172887400-172892600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:172887400-172892800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:172887400-172892800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:172887400-172892800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:172887400-172902800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:172887600-172892400	Weak transcription	HepG2	liver
19	chr2:172887600-172892600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:172887600-172892600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:172887600-172892800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:172887600-172892800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:172888600-172892600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:172888600-172892800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:172890000-172892800	Weak transcription	K562	blood

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