Variant report

Variant	rs6827359
Chromosome Location	chr4:56493940-56493941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:56492253..56496567-chr4:56500430..56503372,5	K562	blood:
2	chr4:56492997..56495090-chr4:56501850..56503549,2	K562	blood:

Variant related genes	Relation type
ENSG00000109255	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10002268	0.88[ASN][1000 genomes]
rs10002541	0.93[CHB][hapmap]
rs10003113	0.88[ASN][1000 genomes]
rs10003211	0.88[ASN][1000 genomes]
rs10011137	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10016506	0.87[CHB][hapmap]
rs10026692	0.93[CHB][hapmap]
rs10033028	0.88[ASN][1000 genomes]
rs10517356	0.88[ASN][1000 genomes]
rs1077103	0.86[ASN][1000 genomes]
rs1077104	0.86[ASN][1000 genomes]
rs11133379	0.87[CHB][hapmap]
rs11133383	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs11133399	0.94[CHB][hapmap];0.89[CHD][hapmap]
rs11133404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726609	0.94[CHB][hapmap];0.92[CHD][hapmap]
rs11735267	0.94[CHB][hapmap]
rs11735910	0.88[ASN][1000 genomes]
rs11931026	0.88[ASN][1000 genomes]
rs11931061	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs11935806	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11939815	0.94[CHB][hapmap]
rs11945558	0.88[ASN][1000 genomes]
rs12498734	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12499623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510588	0.86[ASN][1000 genomes]
rs12512220	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13102385	0.94[CHB][hapmap]
rs13118189	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13121235	0.93[CHB][hapmap]
rs1488939	0.86[ASN][1000 genomes]
rs1522106	0.87[CHB][hapmap];0.92[CHD][hapmap]
rs1522111	1.00[CHB][hapmap]
rs1809643	0.86[ASN][1000 genomes]
rs1844219	0.88[ASN][1000 genomes]
rs1844220	0.88[ASN][1000 genomes]
rs1873092	0.94[CHB][hapmap];0.92[CHD][hapmap]
rs1906677	0.91[ASN][1000 genomes]
rs1971991	0.88[ASN][1000 genomes]
rs2177127	0.94[CHB][hapmap];0.92[CHD][hapmap]
rs2177129	0.94[CHB][hapmap]
rs2412646	0.87[CHB][hapmap]
rs2412663	0.94[CHB][hapmap]
rs28377791	0.97[ASN][1000 genomes]
rs28434169	0.91[ASN][1000 genomes]
rs28448373	0.88[ASN][1000 genomes]
rs28626806	0.88[ASN][1000 genomes]
rs28644417	0.88[ASN][1000 genomes]
rs28694060	1.00[ASN][1000 genomes]
rs2899037	0.94[CHB][hapmap]
rs3736544	0.87[CHB][hapmap]
rs3805154	0.94[CHB][hapmap];0.92[CHD][hapmap]
rs3817444	0.94[CHB][hapmap];0.92[CHD][hapmap]
rs4580704	0.94[CHB][hapmap];0.89[CHD][hapmap]
rs4865010	0.94[CHB][hapmap];0.92[CHD][hapmap]
rs4865018	0.94[CHB][hapmap]
rs4865020	0.89[ASN][1000 genomes]
rs4865021	0.81[ASN][1000 genomes]
rs56268402	0.83[AFR][1000 genomes]
rs61072181	0.98[ASN][1000 genomes]
rs6554286	0.93[CHB][hapmap]
rs6811520	0.87[CHB][hapmap];0.92[CHD][hapmap]
rs6812042	0.94[CHB][hapmap];0.92[CHD][hapmap]
rs6815516	0.94[CHB][hapmap]
rs6823777	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6824955	0.87[CHB][hapmap];0.89[CHD][hapmap]
rs6829182	0.94[CHB][hapmap];0.92[CHD][hapmap]
rs6832769	0.87[CHB][hapmap];0.92[CHD][hapmap]
rs6837710	0.94[CHB][hapmap]
rs6839462	0.85[ASN][1000 genomes]
rs6850524	0.94[CHB][hapmap]
rs6851838	1.00[CHB][hapmap]
rs726967	0.94[CHB][hapmap]
rs7658532	0.88[ASN][1000 genomes]
rs7667849	0.94[CHB][hapmap];0.92[CHD][hapmap]
rs7673908	0.94[CHB][hapmap];0.92[CHD][hapmap]
rs7680941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7684810	0.86[CHB][hapmap]
rs7690375	0.88[ASN][1000 genomes]
rs7690566	0.85[ASN][1000 genomes]
rs7697972	0.86[ASN][1000 genomes]
rs9312662	0.94[CHB][hapmap];0.92[CHD][hapmap]
rs9312664	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9997288	0.94[CHB][hapmap];0.92[CHD][hapmap]
rs9999653	0.98[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv998179	chr4:56425126-56694339	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv932636	chr4:56438618-56667329	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv2762435	chr4:56478362-56494039	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv879021	chr4:56482750-56648713	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3393088	chr4:56484073-56503988	Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3395811	chr4:56486113-56514675	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6827359	SPINK2	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56485400-56498000	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr4:56485400-56498400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:56489400-56498000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:56489800-56498200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:56491600-56496200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:56492000-56496400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:56492200-56495800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:56492200-56498200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:56492200-56498200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:56492400-56496600	Strong transcription	K562	blood
11	chr4:56492600-56498400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:56493400-56500200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:56493800-56494600	Strong transcription	HUES48 Cell Line	embryonic stem cell

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