Variant report

Variant	rs7939784
Chromosome Location	chr11:63910153-63910154
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:63888452..63890195-chr11:63909642..63911388,2	K562	blood:
2	chr11:63907528..63910274-chr11:63911901..63915955,5	K562	blood:
3	chr11:63754724..63756802-chr11:63908470..63911045,2	MCF-7	breast:
4	chr11:63906755..63909220-chr11:63909551..63912410,2	MCF-7	breast:
5	chr11:63909078..63910858-chr11:63932054..63934154,2	MCF-7	breast:
6	chr11:63910019..63912556-chr11:63923747..63925482,2	MCF-7	breast:
7	chr11:63908787..63911048-chr11:63919797..63921636,2	MCF-7	breast:
8	chr11:63908789..63911720-chr11:63932470..63934235,2	MCF-7	breast:
9	chr11:63896044..63898939-chr11:63908774..63911161,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000133315	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1058735	0.86[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.86[EUR][1000 genomes]
rs1059440	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11231701	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11600867	1.00[JPT][hapmap]
rs11601024	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11601577	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11602181	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11603042	0.88[CHB][hapmap]
rs11603212	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11605738	1.00[ASW][hapmap];0.86[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap]
rs11606544	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11607007	0.86[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.86[EUR][1000 genomes]
rs11607144	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11607165	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12418035	0.84[CEU][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12574258	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12575642	1.00[ASW][hapmap];0.86[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12787852	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12794145	1.00[ASW][hapmap];0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.86[EUR][1000 genomes]
rs12797120	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12798333	0.80[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.83[LWK][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs12802950	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2001003	1.00[ASW][hapmap];0.86[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap]
rs2015226	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2070765	1.00[ASW][hapmap];0.86[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.86[EUR][1000 genomes]
rs2154986	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2282490	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2286614	1.00[ASW][hapmap]
rs2875749	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34089806	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34113693	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34838337	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35090903	0.86[EUR][1000 genomes]
rs35095324	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35458188	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35524387	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35858916	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3802933	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3824854	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58632573	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs604203	0.81[CHB][hapmap]
rs6591837	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66648159	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67546972	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7102327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7112277	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7130030	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71479474	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72918475	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72920332	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7944061	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7952318	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs882146	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897630	chr11:63664882-63924446	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
3	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
4	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
5	nsv832184	chr11:63787702-63925084	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
7	nsv832185	chr11:63819946-63963532	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases
8	nsv469961	chr11:63822940-64085967	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
9	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
10	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
11	nsv356	chr11:63868847-63913129	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv897662	chr11:63889749-64150370	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
13	esv1801661	chr11:63894054-63937949	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
14	nsv897663	chr11:63910153-63962152	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	86 gene(s)	inside rSNPs	n/a

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs7939784	CD248	cis	parietal	SCAN
rs7939784	PRDX5	cis	parietal	SCAN
rs7939784	FAM89B	cis	parietal	SCAN
rs7939784	ASRGL1	cis	parietal	SCAN
rs7939784	GPHA2	cis	cerebellum	SCAN
rs7939784	TRPT1	cis	Muscle Skeletal	GTEx
rs7939784	PPP1R14B	Cis_1M	lymphoblastoid	RTeQTL
rs7939784	FKBP2	cis	parietal	SCAN
rs7939784	PPP1R14B	cis	Heart Left Ventricle	GTEx
rs7939784	SLC22A10	cis	parietal	SCAN
rs7939784	FAU	cis	parietal	SCAN
rs7939784	PPP1R14B	cis	multi-tissue	Pritchard

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63885600-63911200	Weak transcription	Gastric	stomach
2	chr11:63890600-63913600	Weak transcription	Esophagus	oesophagus
3	chr11:63892000-63915800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:63895800-63920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:63897200-63918400	Weak transcription	Dnd41	blood
6	chr11:63898800-63916400	Weak transcription	Hela-S3	cervix
7	chr11:63900200-63931800	Weak transcription	Lung	lung
8	chr11:63900400-63916000	Weak transcription	Fetal Intestine Large	intestine
9	chr11:63900800-63916200	Weak transcription	Liver	Liver
10	chr11:63902000-63916600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr11:63902800-63915600	Weak transcription	Fetal Intestine Small	intestine
12	chr11:63903600-63915600	Weak transcription	Left Ventricle	heart
13	chr11:63904200-63913400	Weak transcription	K562	blood
14	chr11:63906200-63913400	Weak transcription	Pancreas	Pancrea
15	chr11:63906800-63911400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:63906800-63912200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:63907000-63915400	Weak transcription	Fetal Heart	heart
18	chr11:63907000-63915600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:63907000-63915600	Weak transcription	Fetal Brain Female	brain
20	chr11:63908600-63910200	Strong transcription	HepG2	liver
21	chr11:63909000-63912000	Weak transcription	Fetal Stomach	stomach
22	chr11:63909400-63911200	Weak transcription	Ovary	ovary
23	chr11:63909400-63911200	Weak transcription	Spleen	Spleen
24	chr11:63909400-63911600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr11:63909400-63912800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr11:63909400-63913000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr11:63909600-63910800	Weak transcription	Brain Germinal Matrix	brain
28	chr11:63909600-63911400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:63909600-63912800	Weak transcription	Brain Hippocampus Middle	brain
30	chr11:63909600-63912800	Weak transcription	Fetal Brain Male	brain
31	chr11:63909600-63912800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr11:63909600-63913000	Weak transcription	Brain Anterior Caudate	brain
33	chr11:63909600-63913000	Weak transcription	Brain Substantia Nigra	brain
34	chr11:63909600-63913000	Weak transcription	Right Ventricle	heart
35	chr11:63909600-63913800	Weak transcription	Fetal Muscle Leg	muscle
36	chr11:63909600-63915400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr11:63909600-63915600	Weak transcription	Psoas Muscle	Psoas
38	chr11:63909600-63916000	Weak transcription	Brain Angular Gyrus	brain
39	chr11:63909800-63912800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr11:63909800-63915400	Weak transcription	Colon Smooth Muscle	Colon

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