Variant report

Variant	rs3136516
Chromosome Location	chr11:46760756-46760757
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:46757054..46759693-chr11:46760177..46761810,2	MCF-7	breast:
2	chr11:46720872..46723638-chr11:46759944..46762583,2	K562	blood:
3	chr11:46760225..46762619-chr11:46766210..46768757,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175220	Chromatin interaction
ENSG00000175213	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11038982	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11038993	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs2306029	0.84[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044225	chr11:46472580-46771102	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv541030	chr11:46472580-46771102	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv430382	chr11:46743135-46849360	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3136516	MADD	cis	parietal	SCAN
rs3136516	C1QTNF4	cis	lymphoblastoid	seeQTL
rs3136516	CHST1	cis	parietal	SCAN
rs3136516	OR4S1	cis	parietal	SCAN
rs3136516	FNBP4	cis	cerebellum	SCAN
rs3136516	ACP2	cis	cerebellum	SCAN
rs3136516	NUP160	cis	cerebellum	SCAN
rs3136516	ACP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46746000-46762800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:46746200-46761200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:46746200-46761400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr11:46749800-46764000	Weak transcription	Aorta	Aorta
5	chr11:46750000-46762800	Weak transcription	Spleen	Spleen
6	chr11:46751200-46761800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:46751200-46762600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:46751400-46762600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:46752000-46762800	Weak transcription	Gastric	stomach
10	chr11:46752000-46763400	Weak transcription	Esophagus	oesophagus
11	chr11:46753000-46786600	Weak transcription	Right Atrium	heart
12	chr11:46757400-46762600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:46757400-46762800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr11:46757800-46762600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:46757800-46762800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr11:46758000-46761400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:46758000-46762600	Weak transcription	Fetal Brain Female	brain
18	chr11:46758200-46761200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:46758200-46761200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr11:46758200-46763200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr11:46758400-46762400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:46758400-46762800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr11:46758400-46763400	Strong transcription	HepG2	liver
24	chr11:46758600-46762800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr11:46758800-46762600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:46758800-46762600	Weak transcription	HUVEC	blood vessel
27	chr11:46758800-46762600	Weak transcription	Osteobl	bone
28	chr11:46758800-46762800	Weak transcription	HMEC	breast
29	chr11:46759000-46762600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr11:46759000-46762600	Weak transcription	Fetal Muscle Leg	muscle
31	chr11:46759000-46762600	Weak transcription	Thymus	Thymus
32	chr11:46759000-46762800	Weak transcription	Primary B cells from cord blood	blood
33	chr11:46759000-46762800	Weak transcription	Pancreas	Pancrea
34	chr11:46759000-46762800	Weak transcription	Hela-S3	cervix
35	chr11:46759000-46763200	Weak transcription	NHLF	lung
36	chr11:46759000-46768000	Strong transcription	Liver	Liver
37	chr11:46759400-46761400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr11:46759400-46762600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr11:46759400-46762800	Weak transcription	Lung	lung
40	chr11:46759400-46762800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr11:46759400-46763200	Weak transcription	NHEK	skin
42	chr11:46759800-46762600	Weak transcription	Brain Germinal Matrix	brain
43	chr11:46759800-46762800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr11:46759800-46762800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr11:46760000-46761600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr11:46760000-46761600	Weak transcription	Fetal Thymus	thymus
47	chr11:46760000-46762400	Weak transcription	Adipose Nuclei	Adipose
48	chr11:46760000-46762600	Weak transcription	Dnd41	blood
49	chr11:46760200-46760800	Enhancers	Ovary	ovary
50	chr11:46760200-46761200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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