Variant report

Variant	rs277647
Chromosome Location	chr3:100074759-100074760
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100052816..100055133-chr3:100074456..100078103,3	MCF-7	breast:
2	chr3:100073604..100075346-chr3:100078489..100080279,2	K562	blood:
3	chr3:100069327..100070989-chr3:100072789..100075380,2	K562	blood:

Variant related genes	Relation type
ENSG00000114021	Chromatin interaction
ENSG00000273488	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1214377	0.83[ASN][1000 genomes]
rs1661287	0.88[ASN][1000 genomes]
rs2289500	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2316264	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277632	0.88[ASN][1000 genomes]
rs277639	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs277641	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6797836	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72941470	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs277647	TOMM70A	Cis_1M	lymphoblastoid	RTeQTL
rs277647	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100054200-100081000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:100054800-100081000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:100054800-100097200	Weak transcription	Stomach Mucosa	stomach
5	chr3:100054800-100102200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:100055000-100082400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:100069400-100082400	Weak transcription	Fetal Brain Male	brain
8	chr3:100069600-100080600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:100069600-100083800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:100069600-100085800	Weak transcription	Small Intestine	intestine
11	chr3:100069600-100087000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:100071000-100074800	Strong transcription	Fetal Brain Female	brain
13	chr3:100071000-100075000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:100071000-100075000	Strong transcription	Stomach Smooth Muscle	stomach
15	chr3:100071000-100075200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:100071000-100075200	Strong transcription	Fetal Thymus	thymus
17	chr3:100071000-100075400	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:100071000-100075400	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:100071000-100075400	Strong transcription	Primary B cells from cord blood	blood
20	chr3:100071000-100075400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:100071000-100075400	Strong transcription	Placenta	Placenta
22	chr3:100071000-100075600	Strong transcription	Primary T cells from cord blood	blood
23	chr3:100071000-100075800	Strong transcription	GM12878-XiMat	blood
24	chr3:100071000-100076400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr3:100071000-100076400	Strong transcription	HSMM	muscle
26	chr3:100071000-100077600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:100071000-100080800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:100071000-100087800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:100071000-100087800	Strong transcription	Fetal Muscle Trunk	muscle
30	chr3:100071000-100093600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:100071000-100103200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:100071000-100104400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:100071200-100074800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:100071200-100074800	Strong transcription	Brain Hippocampus Middle	brain
35	chr3:100071200-100074800	Strong transcription	HMEC	breast
36	chr3:100071200-100075000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr3:100071200-100075000	Strong transcription	Fetal Stomach	stomach
38	chr3:100071200-100075000	Strong transcription	Ovary	ovary
39	chr3:100071200-100075000	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:100071200-100075000	Strong transcription	Thymus	Thymus
41	chr3:100071200-100075200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:100071200-100075200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:100071200-100075200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:100071200-100075200	Strong transcription	Brain Angular Gyrus	brain
45	chr3:100071200-100075200	Strong transcription	Right Ventricle	heart
46	chr3:100071200-100075200	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr3:100071200-100075400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr3:100071200-100075400	Strong transcription	Primary B cells from peripheral blood	blood
49	chr3:100071200-100075400	Strong transcription	Brain Cingulate Gyrus	brain
50	chr3:100071200-100075400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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