Variant report

Variant	rs277639
Chromosome Location	chr3:100087334-100087335
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100087282..100090166-chr3:100119169..100120773,2	K562	blood:
2	chr3:100086232..100088251-chr3:100098253..100100572,2	K562	blood:
3	chr3:100084887..100086773-chr3:100086931..100089034,2	K562	blood:
4	chr3:100083475..100086773-chr3:100086931..100091361,4	K562	blood:
5	chr3:100086102..100087837-chr3:100091620..100093829,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154174	Chromatin interaction
ENSG00000206535	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10936180	0.82[MEX][hapmap]
rs1214377	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1661287	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289500	0.86[ASN][1000 genomes]
rs2316264	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs277632	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277633	0.82[MEX][hapmap]
rs277635	0.82[MEX][hapmap]
rs277638	0.82[MEX][hapmap]
rs277641	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277642	0.82[MEX][hapmap]
rs277647	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs3772692	0.91[MEX][hapmap]
rs6780662	0.82[MEX][hapmap]
rs6794955	0.82[MEX][hapmap]
rs6797836	0.86[ASN][1000 genomes]
rs72941470	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616634	0.82[MEX][hapmap]
rs7641630	0.82[MEX][hapmap]

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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:100054800-100097200	Weak transcription	Stomach Mucosa	stomach
3	chr3:100054800-100102200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:100071000-100087800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:100071000-100087800	Strong transcription	Fetal Muscle Trunk	muscle
6	chr3:100071000-100093600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:100071000-100103200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:100071000-100104400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:100071400-100088000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:100071400-100105800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:100071800-100090600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:100073200-100090200	Weak transcription	Esophagus	oesophagus
13	chr3:100073400-100090400	Weak transcription	Pancreas	Pancrea
14	chr3:100073400-100096400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:100073800-100090600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:100073800-100098200	Weak transcription	Gastric	stomach
17	chr3:100077000-100106000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr3:100077200-100088000	Strong transcription	Primary B cells from cord blood	blood
19	chr3:100077200-100105600	Strong transcription	Duodenum Mucosa	Duodenum
20	chr3:100077600-100105200	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:100078400-100089600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:100078600-100087600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:100078800-100087800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:100078800-100103000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:100078800-100104400	Strong transcription	Fetal Intestine Large	intestine
26	chr3:100079000-100092200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:100079200-100088200	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr3:100079400-100103200	Strong transcription	Osteobl	bone
29	chr3:100079400-100107600	Strong transcription	Dnd41	blood
30	chr3:100079600-100087600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:100079600-100088000	Strong transcription	Fetal Lung	lung
32	chr3:100079600-100088600	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:100079600-100091800	Strong transcription	Fetal Muscle Leg	muscle
34	chr3:100079600-100106200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr3:100079800-100093200	Strong transcription	Fetal Thymus	thymus
36	chr3:100079800-100106200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:100080000-100087800	Strong transcription	Fetal Brain Female	brain
38	chr3:100080200-100088000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:100080200-100104400	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:100080200-100106200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr3:100080600-100105800	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:100080800-100092400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr3:100081000-100092400	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr3:100081000-100092800	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:100081000-100094800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr3:100081000-100104000	Weak transcription	Aorta	Aorta
47	chr3:100081000-100106000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:100081200-100087400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:100081200-100088000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:100081200-100088000	Strong transcription	GM12878-XiMat	blood

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