Variant report

Variant	rs11681005
Chromosome Location	chr2:172889613-172889614
allele	C/T
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	chr2:172866012..172868252-chr2:172888365..172889925,2	K562	blood:
3	chr2:172885240..172888005-chr2:172889269..172891539,4	MCF-7	breast:
4	chr2:172888478..172891307-chr2:172961439..172963560,3	K562	blood:

Variant related genes	Relation type
ENSG00000172878	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11673986	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11675404	0.82[ASW][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap]
rs11688839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11695630	0.82[ASW][hapmap];0.87[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12988345	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12988675	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12989544	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12996935	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13013988	0.87[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs17500199	0.85[JPT][hapmap]
rs1965159	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34137430	0.82[AFR][1000 genomes]
rs56041936	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62182435	0.82[AFR][1000 genomes]
rs62183768	0.82[AFR][1000 genomes]
rs62183773	0.82[AFR][1000 genomes]
rs62183803	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62183807	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62183812	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62183813	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7580363	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11681005	B3GALT1	cis	cerebellum	SCAN
rs11681005	SLC25A12	cis	parietal	SCAN
rs11681005	SLC25A12	cis	cerebellum	SCAN
rs11681005	MAP1D	cis	parietal	SCAN

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	chr2:172888000-172890000	Enhancers	K562	blood
24	chr2:172888600-172892600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:172888600-172892800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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