Variant report

Variant	rs2078164
Chromosome Location	chr11:34370840-34370841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:34365763..34368722-chr11:34368922..34370946,2	MCF-7	breast:
2	chr11:34368701..34370901-chr11:34379752..34381357,2	K562	blood:
3	chr11:34194734..34196633-chr11:34370779..34372924,2	MCF-7	breast:
4	chr11:34368537..34371450-chr11:34371767..34375088,3	K562	blood:
5	chr11:34331497..34333782-chr11:34370435..34371982,2	MCF-7	breast:
6	chr11:34370190..34372687-chr11:34377981..34381177,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166016	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10734424	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10734425	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1269119	0.81[CEU][hapmap]
rs1886656	0.80[EUR][1000 genomes]
rs2009036	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2078165	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2745915	0.85[JPT][hapmap]
rs2755148	0.81[CEU][hapmap]
rs4756137	0.85[JPT][hapmap]
rs6484707	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7944742	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897205	chr11:34248229-34507213	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897207	chr11:34253683-34621004	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv897208	chr11:34257064-34562247	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv897209	chr11:34309519-34548906	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv897210	chr11:34349427-34381075	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2078164	SNORA71B	trans	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34363000-34372400	Enhancers	Fetal Muscle Leg	muscle
2	chr11:34364200-34376600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:34364400-34371000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr11:34365400-34372200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr11:34366000-34371800	Enhancers	Right Atrium	heart
6	chr11:34366200-34371200	Enhancers	Fetal Stomach	stomach
7	chr11:34366400-34374000	Enhancers	Psoas Muscle	Psoas
8	chr11:34367000-34371800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:34367000-34376200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr11:34367200-34375200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:34367400-34376400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr11:34367600-34372800	Enhancers	HepG2	liver
13	chr11:34367800-34376400	Weak transcription	Pancreas	Pancrea
14	chr11:34368200-34373000	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr11:34368200-34375000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr11:34368200-34376600	Weak transcription	Brain Angular Gyrus	brain
17	chr11:34368400-34371000	Enhancers	Fetal Heart	heart
18	chr11:34368400-34372200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr11:34368400-34375800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr11:34368400-34376200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:34368400-34377800	Weak transcription	Gastric	stomach
22	chr11:34368600-34371200	Weak transcription	NH-A	brain
23	chr11:34368600-34371400	Enhancers	Stomach Smooth Muscle	stomach
24	chr11:34368600-34371400	Enhancers	A549	lung
25	chr11:34368600-34372000	Enhancers	HSMM	muscle
26	chr11:34368600-34373200	Enhancers	HSMMtube	muscle
27	chr11:34368600-34374200	Weak transcription	Stomach Mucosa	stomach
28	chr11:34368600-34376400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:34368800-34371200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr11:34368800-34371400	Weak transcription	Hela-S3	cervix
31	chr11:34368800-34374800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr11:34368800-34376200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr11:34368800-34376200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:34369000-34371800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr11:34369400-34372200	Enhancers	Left Ventricle	heart
36	chr11:34369400-34372800	Enhancers	Liver	Liver
37	chr11:34370000-34371000	Enhancers	Fetal Thymus	thymus
38	chr11:34370000-34371200	Enhancers	Thymus	Thymus
39	chr11:34370000-34371400	Enhancers	Colon Smooth Muscle	Colon
40	chr11:34370000-34372200	Enhancers	Right Ventricle	heart
41	chr11:34370200-34371400	Weak transcription	Placenta	Placenta
42	chr11:34370200-34372000	Enhancers	Brain Hippocampus Middle	brain
43	chr11:34370200-34372600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr11:34370400-34371000	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr11:34370400-34371000	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr11:34370400-34371200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:34370400-34371400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr11:34370400-34371400	Weak transcription	Aorta	Aorta
49	chr11:34370400-34371800	Enhancers	Brain Substantia Nigra	brain
50	chr11:34370600-34371000	Weak transcription	Small Intestine	intestine

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