Variant report

Variant	rs2096706
Chromosome Location	chr11:63924446-63924447
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:63910019..63912556-chr11:63923747..63925482,2	MCF-7	breast:
2	chr11:63924134..63929191-chr11:63930561..63934852,10	K562	blood:
3	chr11:63921851..63923670-chr11:63924013..63926369,2	MCF-7	breast:
4	chr11:63779610..63782296-chr11:63923822..63926567,2	MCF-7	breast:
5	chr11:63923167..63927304-chr11:63949302..63952377,3	MCF-7	breast:
6	chr11:63731448..63734435-chr11:63923552..63925459,2	MCF-7	breast:
7	chr11:63922444..63925519-chr11:63951476..63954274,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168439	Chromatin interaction
ENSG00000133315	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1011219	0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11231710	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11231713	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231726	0.82[CHD][hapmap];0.84[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs11600628	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11600667	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11604083	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11605193	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11605856	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11607903	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12417635	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12419038	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs17773078	0.85[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2005272	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2186572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3862371	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55942618	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55970968	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56207008	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56311067	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57021319	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60394481	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61083753	0.82[EUR][1000 genomes]
rs646384	1.00[ASW][hapmap];0.87[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap]
rs660070	1.00[ASW][hapmap]
rs683996	0.81[TSI][hapmap]
rs7103915	0.81[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7109921	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7122408	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7123026	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs734762	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7941773	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs876064	1.00[ASW][hapmap];0.89[JPT][hapmap]
rs915987	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[JPT][hapmap]
rs947939	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
12	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
13	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
14	nsv897664	chr11:63919742-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh 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	237 gene(s)	inside rSNPs	diseases
15	nsv468592	chr11:63924446-64042997	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	166 gene(s)	inside rSNPs	diseases
16	nsv555184	chr11:63924446-64042997	Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	166 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2096706	RAB1B	cis	cerebellum	SCAN
rs2096706	RBM14	cis	cerebellum	SCAN
rs2096706	CCDC88B	cis	cerebellum	SCAN
rs2096706	NUDT22	Cis_1M	lymphoblastoid	RTeQTL
rs2096706	RCE1	cis	cerebellum	SCAN
rs2096706	CCS	cis	cerebellum	SCAN
rs2096706	FKBP2	cis	parietal	SCAN
rs2096706	FKBP2	cis	cerebellum	SCAN
rs2096706	CCDC88B	cis	lymphoblastoid	seeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63900200-63931800	Weak transcription	Lung	lung
2	chr11:63911600-63932600	Weak transcription	Primary T cells from cord blood	blood
3	chr11:63916200-63932000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr11:63916400-63932000	Weak transcription	Stomach Mucosa	stomach
5	chr11:63916600-63932200	Weak transcription	Fetal Intestine Large	intestine
6	chr11:63918200-63932200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr11:63918600-63931800	Weak transcription	Gastric	stomach
8	chr11:63919000-63932000	Weak transcription	Adipose Nuclei	Adipose
9	chr11:63919200-63928800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr11:63920000-63925600	Weak transcription	Fetal Intestine Small	intestine
11	chr11:63920200-63931800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr11:63920600-63925000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:63920600-63925400	Weak transcription	Psoas Muscle	Psoas
14	chr11:63920600-63928600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr11:63920600-63928800	Weak transcription	Aorta	Aorta
16	chr11:63920600-63931800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:63920600-63931800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr11:63920600-63932200	Weak transcription	Brain Substantia Nigra	brain
19	chr11:63920600-63932200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr11:63920600-63932400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:63920600-63932400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr11:63920800-63925600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr11:63920800-63931800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr11:63920800-63931800	Weak transcription	Liver	Liver
25	chr11:63920800-63931800	Weak transcription	Colonic Mucosa	Colon
26	chr11:63920800-63932000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:63921000-63925400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr11:63921000-63931600	Weak transcription	Dnd41	blood
29	chr11:63921000-63931800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr11:63921000-63932000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr11:63921000-63932200	Weak transcription	Small Intestine	intestine
32	chr11:63921000-63932400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr11:63921000-63932400	Weak transcription	A549	lung
34	chr11:63921200-63927200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:63921400-63932200	Weak transcription	Esophagus	oesophagus
36	chr11:63921600-63925200	Weak transcription	Right Ventricle	heart
37	chr11:63921600-63929600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr11:63921800-63925600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:63921800-63932000	Weak transcription	Ovary	ovary
40	chr11:63921800-63932200	Weak transcription	K562	blood
41	chr11:63922000-63931800	Weak transcription	Brain Germinal Matrix	brain
42	chr11:63922000-63932200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr11:63922000-63932200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:63922200-63932200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:63922600-63930400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr11:63923600-63924800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr11:63923600-63927400	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr11:63923800-63924600	Enhancers	Left Ventricle	heart
49	chr11:63923800-63925400	Enhancers	HepG2	liver
50	chr11:63923800-63925600	Enhancers	Fetal Heart	heart

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