Variant report

Variant	rs4678405
Chromosome Location	chr3:137966646-137966647
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:137906393..137908040-chr3:137965617..137967186,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114098	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13065895	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs329387	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs3773766	0.92[CEU][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6778511	0.89[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6805348	0.81[CHD][hapmap]
rs7612622	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7631734	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774800	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap]
rs774801	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs939453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9822008	0.84[EUR][1000 genomes]
rs9842193	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9853581	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9862439	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][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	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877536	chr3:137870523-137970907	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137940200-137970600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:137940400-137969200	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:137940400-137970600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:137940600-137971200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:137941000-137968200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:137941000-137968600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:137941600-137967200	Strong transcription	Dnd41	blood
8	chr3:137941600-137968000	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr3:137941800-137966800	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:137942000-137968000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:137942200-137967800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:137942400-137970600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:137942600-137968600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:137942600-137970600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr3:137942800-137993400	Weak transcription	Fetal Brain Male	brain
16	chr3:137943600-137992000	Weak transcription	Gastric	stomach
17	chr3:137944200-137992000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:137944600-137971400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:137944800-137967600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:137944800-137984400	Weak transcription	Spleen	Spleen
21	chr3:137944800-138017400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:137945000-137976200	Weak transcription	Psoas Muscle	Psoas
23	chr3:137946200-137991800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:137946600-137969000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:137947400-137967600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:137947400-137968800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:137947600-137968400	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:137950000-137972400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:137950800-137992000	Weak transcription	NHLF	lung
30	chr3:137951000-137977600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:137951200-137992000	Weak transcription	Pancreas	Pancrea
32	chr3:137952000-137966800	Weak transcription	Fetal Heart	heart
33	chr3:137952200-137984400	Weak transcription	Aorta	Aorta
34	chr3:137952200-137992000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:137952400-137984400	Weak transcription	Brain Angular Gyrus	brain
36	chr3:137953200-137967400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr3:137953400-137967400	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:137953400-137967800	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:137953400-137967800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:137953600-137967800	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr3:137953600-137992000	Weak transcription	Colonic Mucosa	Colon
42	chr3:137953800-137966800	Strong transcription	Placenta	Placenta
43	chr3:137953800-137968000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:137953800-137968800	Strong transcription	Primary hematopoietic stem cells	blood
45	chr3:137954000-137968200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:137954200-137968000	Strong transcription	HSMM	muscle
47	chr3:137954400-137967600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:137954600-138014400	Weak transcription	NHDF-Ad	bronchial
49	chr3:137955600-137977600	Weak transcription	Lung	lung
50	chr3:137955600-137984600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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