Variant report

Variant	rs3768777
Chromosome Location	chr2:187456121-187456122
allele	A/G
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	chr2:187370485..187373217-chr2:187453776..187456177,3	MCF-7	breast:
2	chr2:187360313..187361827-chr2:187456108..187458564,2	K562	blood:
3	chr2:187349672..187352615-chr2:187454696..187458504,4	K562	blood:
4	chr2:187418262..187420744-chr2:187454965..187457537,2	MCF-7	breast:
5	chr2:187350028..187353171-chr2:187452977..187457092,6	MCF-7	breast:
6	chr2:187454844..187457492-chr2:187557694..187560224,2	K562	blood:
7	chr2:187370609..187373386-chr2:187454442..187456199,2	MCF-7	breast:
8	chr2:187350319..187353074-chr2:187452754..187457832,8	K562	blood:
9	chr2:187367976..187370185-chr2:187454691..187457440,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000227227	Chromatin interaction
ENSG00000065548	Chromatin interaction
ENSG00000144369	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10171481	0.86[CHB][hapmap]
rs10174098	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10804007	0.86[CHB][hapmap]
rs13006571	0.86[CHB][hapmap]
rs1992898	0.86[CHB][hapmap]
rs2165656	0.86[CHB][hapmap]
rs2197138	0.86[CHB][hapmap]
rs2197787	0.86[CHB][hapmap];0.86[YRI][hapmap]
rs2370693	0.86[CHB][hapmap]
rs2595375	0.86[CHB][hapmap]
rs2887827	0.86[CHB][hapmap]
rs3768778	0.86[CHB][hapmap]
rs3768780	0.86[CHB][hapmap];0.86[YRI][hapmap]
rs3911084	0.84[ASW][hapmap];0.86[CHB][hapmap]
rs3911239	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4233788	0.86[CHB][hapmap]
rs6741369	0.86[CHB][hapmap]
rs7596996	0.86[CHB][hapmap]
rs9333287	0.86[CHB][hapmap];0.85[YRI][hapmap]
rs9333288	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv875552	chr2:187393729-187505486	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1014203	chr2:187413781-187477586	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv536083	chr2:187413781-187477586	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	esv2756507	chr2:187416494-187470494	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	esv2756956	chr2:187416599-187492742	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	nsv818105	chr2:187423298-187481835	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	esv2753217	chr2:187424494-187470494	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3768777	ITGAV	cis	cerebellum	SCAN
rs3768777	ITGAV	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187453400-187456800	Active TSS	Fetal Brain Female	brain
2	chr2:187453600-187456400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:187453600-187458800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:187453800-187456400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:187453800-187456400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr2:187453800-187456400	Active TSS	Psoas Muscle	Psoas
7	chr2:187453800-187456400	Active TSS	Stomach Mucosa	stomach
8	chr2:187453800-187456600	Active TSS	Brain Anterior Caudate	brain
9	chr2:187453800-187456600	Active TSS	Brain Hippocampus Middle	brain
10	chr2:187453800-187457400	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr2:187453800-187458000	Active TSS	Right Ventricle	heart
12	chr2:187454000-187456200	Active TSS	Fetal Kidney	kidney
13	chr2:187454000-187456400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr2:187454000-187456400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:187454000-187456400	Active TSS	Fetal Muscle Trunk	muscle
16	chr2:187454000-187456400	Active TSS	Placenta	Placenta
17	chr2:187454000-187456400	Active TSS	Lung	lung
18	chr2:187454000-187456600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:187454000-187456600	Active TSS	Colonic Mucosa	Colon
20	chr2:187454000-187456600	Active TSS	Ovary	ovary
21	chr2:187454000-187456800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:187454000-187456800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:187454000-187456800	Active TSS	Fetal Intestine Large	intestine
24	chr2:187454000-187456800	Active TSS	NHDF-Ad	bronchial
25	chr2:187454000-187457000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:187454000-187457000	Active TSS	Left Ventricle	heart
27	chr2:187454000-187457200	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr2:187454000-187457200	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr2:187454000-187457200	Active TSS	A549	lung
30	chr2:187454200-187456200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr2:187454200-187456200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:187454200-187456200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:187454200-187456200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:187454200-187456200	Active TSS	Esophagus	oesophagus
35	chr2:187454200-187456200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr2:187454200-187456200	Active TSS	Fetal Lung	lung
37	chr2:187454200-187456200	Active TSS	Fetal Thymus	thymus
38	chr2:187454200-187456200	Active TSS	Pancreas	Pancrea
39	chr2:187454200-187456200	Active TSS	Rectal Smooth Muscle	rectum
40	chr2:187454200-187456400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:187454200-187456400	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr2:187454200-187456400	Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr2:187454200-187456400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:187454200-187456400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:187454200-187456400	Active TSS	Colon Smooth Muscle	Colon
46	chr2:187454200-187456400	Active TSS	Osteobl	bone
47	chr2:187454200-187456600	Active TSS	H1 Cell Line	embryonic stem cell
48	chr2:187454200-187456600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:187454200-187456600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:187454200-187456600	Active TSS	Aorta	Aorta

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