Variant report

Variant	rs1873250
Chromosome Location	chr6:34022740-34022741
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34022571..34024055-chr6:34122245..34123197,6	MCF-7	breast:
2	chr6:33736439..33736983-chr6:34022692..34023404,3	K562	blood:
3	chr6:33739026..33739542-chr6:34022697..34023340,2	K562	blood:
4	chr6:33679645..33680333-chr6:34022737..34023251,2	K562	blood:
5	chr6:34007682..34010620-chr6:34022223..34024070,2	K562	blood:
6	chr6:34020794..34023271-chr6:34122578..34124489,2	K562	blood:

Variant related genes	Relation type
ENSG00000124493	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12111392	0.93[EUR][1000 genomes]
rs12663035	0.81[EUR][1000 genomes]
rs12664932	0.81[EUR][1000 genomes]
rs1565365	0.81[EUR][1000 genomes]
rs1565366	0.81[EUR][1000 genomes]
rs1873254	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2229900	0.94[EUR][1000 genomes]
rs2395554	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2451358	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2451381	0.82[EUR][1000 genomes]
rs2451382	0.85[EUR][1000 genomes]
rs2451383	0.84[CEU][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs2451384	0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2451385	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2451386	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2451387	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2499672	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2499673	0.84[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2499674	0.88[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2499675	0.81[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2499676	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2499677	0.84[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3103432	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35075443	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35411382	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3734361	0.81[EUR][1000 genomes]
rs3778068	0.85[YRI][hapmap]
rs3798529	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4713735	0.81[EUR][1000 genomes]
rs4713736	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6901097	0.84[YRI][hapmap]
rs6922166	0.81[EUR][1000 genomes]
rs71556962	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7772059	0.80[EUR][1000 genomes]
rs7775780	0.81[EUR][1000 genomes]
rs9366837	0.81[EUR][1000 genomes]
rs9394185	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9461949	0.81[EUR][1000 genomes]
rs9469690	0.81[EUR][1000 genomes]
rs9469691	0.81[EUR][1000 genomes]
rs9469697	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916210	chr6:33804111-34144062	Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv462900	chr6:33932442-34195011	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv602843	chr6:33932442-34195011	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
4	nsv462901	chr6:33953646-34050917	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
5	nsv602861	chr6:33953646-34050917	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1873250	NUDT3	cis	parietal	SCAN
rs1873250	TMEM217	cis	parietal	SCAN
rs1873250	GRM4	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33984400-34023000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:34002800-34027000	Weak transcription	Spleen	Spleen
3	chr6:34016800-34024600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:34019800-34023200	Weak transcription	K562	blood
5	chr6:34020400-34023400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:34020600-34024000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr6:34020800-34025200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr6:34021000-34024200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:34021000-34025200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:34021200-34022800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr6:34021400-34023200	Weak transcription	Esophagus	oesophagus
12	chr6:34021800-34023000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:34021800-34023800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:34021800-34024000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:34022000-34023200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:34022000-34023600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:34022400-34024800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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