Variant report

Variant	rs1182864
Chromosome Location	chr6:39230307-39230308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:39223708..39225887-chr6:39227549..39230427,2	MCF-7	breast:
2	chr6:39196024..39198619-chr6:39228608..39230535,2	K562	blood:
3	chr6:39195258..39199147-chr6:39228497..39232798,6	MCF-7	breast:
4	chr6:39228773..39231561-chr6:39235112..39238664,3	K562	blood:

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1005995	0.83[ASN][1000 genomes]
rs12191604	0.89[ASN][1000 genomes]
rs12191756	0.89[ASN][1000 genomes]
rs12194951	0.84[MKK][hapmap];1.00[YRI][hapmap]
rs12214600	1.00[LWK][hapmap]
rs2253582	0.89[CHB][hapmap];0.89[ASN][1000 genomes]
rs2395719	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2395720	0.90[ASN][1000 genomes]
rs2758864	0.89[ASN][1000 genomes]
rs2758865	0.88[ASN][1000 genomes]
rs2758866	0.89[ASN][1000 genomes]
rs2758867	0.89[ASN][1000 genomes]
rs2758868	0.88[ASN][1000 genomes]
rs2758869	0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs2758871	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs2758872	0.85[ASN][1000 genomes]
rs2758874	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs2758912	0.86[GIH][hapmap]
rs2815019	0.90[CHB][hapmap];0.93[CHD][hapmap];0.89[ASN][1000 genomes]
rs2815020	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs2815024	0.89[ASN][1000 genomes]
rs2815025	0.89[ASN][1000 genomes]
rs2815026	0.89[ASN][1000 genomes]
rs2815027	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2815028	0.89[ASN][1000 genomes]
rs2815029	0.89[ASN][1000 genomes]
rs2815030	0.94[ASN][1000 genomes]
rs2815031	0.89[ASN][1000 genomes]
rs2815032	0.89[ASN][1000 genomes]
rs2815035	0.89[ASN][1000 genomes]
rs2815036	0.89[ASN][1000 genomes]
rs2815037	0.90[CHB][hapmap];0.89[ASN][1000 genomes]
rs2815038	0.89[ASN][1000 genomes]
rs2815039	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs2815040	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs2815041	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs2815042	0.90[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs2815044	0.85[ASN][1000 genomes]
rs2815045	0.81[ASN][1000 genomes]
rs2815061	0.81[ASN][1000 genomes]
rs34170020	0.86[ASN][1000 genomes]
rs34343201	0.86[ASN][1000 genomes]
rs4714233	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7746595	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9394580	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9394581	0.83[MKK][hapmap];1.00[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	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active 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 miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv519606	chr6:39229763-39230571	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1182864	LOC221442	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39224400-39231000	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr6:39224400-39238400	Weak transcription	Spleen	Spleen
3	chr6:39224600-39230800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:39225000-39231000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:39227200-39231000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:39227200-39236000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:39227800-39230600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:39228400-39234600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:39229000-39230400	Enhancers	Fetal Intestine Small	intestine
10	chr6:39229000-39231400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:39229000-39231800	Enhancers	Fetal Intestine Large	intestine
12	chr6:39229200-39230400	Enhancers	H1 Cell Line	embryonic stem cell
13	chr6:39229200-39230400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr6:39229400-39231000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr6:39229600-39230400	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr6:39229800-39230800	Weak transcription	Liver	Liver
17	chr6:39230000-39235000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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