Variant report

Variant	rs2952172
Chromosome Location	chr8:10130696-10130697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:9911202..9913645-chr8:10128676..10130785,2	MCF-7	breast:
2	chr8:10130155..10132980-chr8:10133293..10136060,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260093	Chromatin interaction
ENSG00000175806	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11249980	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17151637	0.82[GIH][hapmap]
rs2009619	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2952168	0.85[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2952176	0.85[EUR][1000 genomes]
rs2952183	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs2952184	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs2952186	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2952187	0.86[AFR][1000 genomes]
rs2952228	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2952251	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2952254	0.80[TSI][hapmap]
rs2952257	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2952258	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2952262	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2975635	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2975647	0.93[ASW][hapmap];0.88[CHB][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2975648	0.89[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2975649	0.93[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2975653	0.85[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2975654	1.00[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2975655	0.85[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2975662	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2975675	0.81[AFR][1000 genomes]
rs2975680	0.96[YRI][hapmap]
rs2975682	0.92[YRI][hapmap]
rs4260895	0.90[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4841305	0.89[YRI][hapmap]
rs6601426	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs6601443	0.85[CEU][hapmap]
rs7818437	0.81[CEU][hapmap]
rs7838901	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831230	chr8:9953343-10139350	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1021921	chr8:9958259-10212555	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv831231	chr8:10001214-10189094	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1026335	chr8:10037279-10139782	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1016347	chr8:10091475-10223667	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1028650	chr8:10101815-10178537	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2952172	XKR6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10123000-10138400	Weak transcription	Spleen	Spleen
2	chr8:10123600-10135400	Weak transcription	Fetal Intestine Small	intestine
3	chr8:10125600-10136000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr8:10126600-10132400	Enhancers	Fetal Brain Male	brain
5	chr8:10128200-10137000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr8:10128400-10132200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr8:10128400-10133600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr8:10128400-10138200	Weak transcription	Fetal Brain Female	brain
9	chr8:10129000-10133000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr8:10129000-10133200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr8:10129600-10130800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr8:10130200-10132200	Weak transcription	Brain Germinal Matrix	brain
13	chr8:10130400-10133400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr8:10130400-10144200	Weak transcription	Liver	Liver
15	chr8:10130600-10131400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr8:10130600-10133600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr8:10130600-10137600	Weak transcription	Primary T cells from cord blood	blood

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