Variant report

Variant	rs905604
Chromosome Location	chr3:100472848-100472849
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100468053..100471019-chr3:100472317..100474592,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1144105	1.00[YRI][hapmap]
rs1144108	1.00[YRI][hapmap]
rs1144126	1.00[YRI][hapmap]
rs1145348	1.00[YRI][hapmap]
rs1718279	1.00[YRI][hapmap]
rs586347	1.00[YRI][hapmap]
rs610854	1.00[YRI][hapmap]
rs6441552	0.82[YRI][hapmap]
rs900234	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751968	chr3:100299329-100476713	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv432466	chr3:100299329-100476713	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv2751969	chr3:100312499-100479384	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers 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 target site	18 gene(s)	inside rSNPs	diseases
4	esv2751972	chr3:100342493-100493062	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers 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 target site	18 gene(s)	inside rSNPs	diseases
5	nsv432469	chr3:100342493-100493062	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv2751973	chr3:100354170-100476713	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer 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
7	esv2751974	chr3:100354170-100476713	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	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
rs905604	TFG	cis	multi-tissue	Pritchard
rs905604	ST3GAL6	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100429800-100475000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:100430400-100473000	Strong transcription	Fetal Thymus	thymus
3	chr3:100431200-100473000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:100432400-100474400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr3:100432800-100473600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:100434400-100478200	Weak transcription	Spleen	Spleen
7	chr3:100436000-100474400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:100436800-100473000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:100437600-100475000	Strong transcription	Placenta	Placenta
10	chr3:100437800-100474400	Strong transcription	Duodenum Mucosa	Duodenum
11	chr3:100438800-100473800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:100441000-100473000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:100441000-100474400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:100441000-100479400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:100444600-100474400	Strong transcription	HSMM	muscle
16	chr3:100445400-100473800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:100445400-100475600	Weak transcription	Pancreas	Pancrea
18	chr3:100447400-100473600	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr3:100447600-100474200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:100447600-100477200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:100448600-100474400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:100450000-100501000	Weak transcription	Esophagus	oesophagus
23	chr3:100453200-100479000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:100453600-100473000	Weak transcription	Stomach Mucosa	stomach
25	chr3:100457200-100473600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:100457200-100474800	Strong transcription	NHDF-Ad	bronchial
27	chr3:100457200-100480200	Weak transcription	Brain Angular Gyrus	brain
28	chr3:100458000-100473600	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:100459200-100474600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:100459400-100478200	Weak transcription	Fetal Stomach	stomach
31	chr3:100459600-100473000	Weak transcription	Small Intestine	intestine
32	chr3:100463000-100473000	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr3:100463000-100473400	Strong transcription	Primary B cells from cord blood	blood
34	chr3:100463000-100474400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:100463000-100474400	Strong transcription	Adipose Nuclei	Adipose
36	chr3:100463400-100473600	Strong transcription	Fetal Muscle Trunk	muscle
37	chr3:100463600-100474800	Strong transcription	HSMMtube	muscle
38	chr3:100464200-100473600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:100464400-100473000	Strong transcription	GM12878-XiMat	blood
40	chr3:100464600-100473400	Strong transcription	A549	lung
41	chr3:100464600-100473400	Strong transcription	Osteobl	bone
42	chr3:100465600-100478000	Weak transcription	Aorta	Aorta
43	chr3:100465600-100478000	Weak transcription	Fetal Heart	heart
44	chr3:100466800-100473800	Strong transcription	Fetal Intestine Large	intestine
45	chr3:100467000-100474400	Strong transcription	Primary T cells from cord blood	blood
46	chr3:100467400-100474400	Weak transcription	Fetal Brain Female	brain
47	chr3:100467400-100475800	Weak transcription	Thymus	Thymus
48	chr3:100467400-100497600	Weak transcription	Fetal Intestine Small	intestine
49	chr3:100467600-100473800	Weak transcription	Ovary	ovary
50	chr3:100467800-100474200	Weak transcription	Colonic Mucosa	Colon

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