Variant report

Variant	rs7621604
Chromosome Location	chr3:61557718-61557719
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:61554363..61558137-chr3:61559653..61562085,4	MCF-7	breast:
2	chr3:61556565..61559490-chr3:61559531..61561160,2	MCF-7	breast:
3	chr3:61546018..61548873-chr3:61556262..61559991,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144724	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs35668148	0.82[ASN][1000 genomes]
rs6445225	0.89[GIH][hapmap]
rs6789675	0.82[ASN][1000 genomes]
rs9828525	0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv834711	chr3:61413762-61612539	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1008615	chr3:61455419-61679037	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7621604	FAM107A	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61550600-61568600	Weak transcription	Pancreas	Pancrea
2	chr3:61550800-61558400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:61550800-61574200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:61551000-61559800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:61551000-61559800	Weak transcription	NHEK	skin
6	chr3:61551000-61561600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:61551200-61560000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:61551600-61559800	Weak transcription	NHLF	lung
9	chr3:61551600-61563800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:61552200-61563400	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:61553000-61558200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:61553400-61559800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:61553600-61558200	Weak transcription	Lung	lung
14	chr3:61553600-61566400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:61555400-61558000	Enhancers	Adipose Nuclei	Adipose
16	chr3:61555400-61558200	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:61555400-61560000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:61555600-61560200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:61555800-61559800	Enhancers	Osteobl	bone
20	chr3:61556200-61558200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr3:61556200-61558800	Enhancers	HSMM	muscle
22	chr3:61556200-61559800	Weak transcription	Fetal Lung	lung
23	chr3:61556200-61564000	Weak transcription	HepG2	liver
24	chr3:61556600-61560800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr3:61556800-61557800	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr3:61556800-61558000	Enhancers	NHDF-Ad	bronchial
27	chr3:61556800-61558200	Enhancers	NH-A	brain
28	chr3:61556800-61559200	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr3:61556800-61560600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:61556800-61561000	Enhancers	Right Ventricle	heart
31	chr3:61557000-61557800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr3:61557000-61557800	Enhancers	HUVEC	blood vessel
33	chr3:61557000-61558000	Enhancers	HSMMtube	muscle
34	chr3:61557000-61559000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr3:61557000-61559200	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr3:61557000-61561600	Weak transcription	Ovary	ovary
37	chr3:61557200-61557800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:61557200-61557800	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr3:61557200-61557800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:61557200-61557800	Enhancers	HMEC	breast
41	chr3:61557400-61557800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:61557400-61557800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr3:61557400-61557800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr3:61557400-61558000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:61557400-61558200	Enhancers	H9 Cell Line	embryonic stem cell
46	chr3:61557400-61558800	Enhancers	Left Ventricle	heart
47	chr3:61557400-61561000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr3:61557600-61557800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr3:61557600-61557800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:61557600-61557800	Enhancers	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links