Variant report

Variant	rs327111
Chromosome Location	chr4:187606984-187606985
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:187605170..187608149-chr4:187626258..187628556,2	MCF-7	breast:
2	chr4:187598530..187601014-chr4:187604805..187607221,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs162063	0.84[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs162182	1.00[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs167854	0.84[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs192997	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28532777	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs327067	0.88[CHB][hapmap]
rs327077	0.84[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs327078	1.00[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3733409	0.87[CHB][hapmap]
rs3733415	0.82[CHB][hapmap]
rs456000	0.84[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs462509	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818461	0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025088	chr4:187407683-187674585	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1025244	chr4:187419770-188284813	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1034212	chr4:187437895-188030805	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv537438	chr4:187437895-188030805	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv532745	chr4:187471692-188205443	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv1022262	chr4:187475862-187848284	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1024705	chr4:187534005-187849091	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1026970	chr4:187537418-187913351	Weak transcription Enhancers Active TSS Strong transcription Flanking 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	15 gene(s)	inside rSNPs	diseases
9	nsv596440	chr4:187538133-187848075	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv881509	chr4:187574398-187614434	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs327111	FAM149A	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:187583000-187614400	Weak transcription	Colonic Mucosa	Colon
2	chr4:187587600-187610200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:187591200-187607000	Weak transcription	Adipose Nuclei	Adipose
4	chr4:187591200-187614400	Weak transcription	Ovary	ovary
5	chr4:187598200-187614400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:187598400-187609400	Weak transcription	Aorta	Aorta
7	chr4:187600200-187617000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr4:187603800-187607000	Enhancers	Left Ventricle	heart
9	chr4:187603800-187609000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr4:187604000-187608400	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr4:187604200-187608800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr4:187604400-187611600	Enhancers	Fetal Lung	lung
13	chr4:187604600-187607400	Enhancers	Fetal Muscle Leg	muscle
14	chr4:187604600-187618000	Weak transcription	Fetal Stomach	stomach
15	chr4:187604600-187626800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:187605000-187610400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr4:187605200-187607800	Flanking Active TSS	HepG2	liver
18	chr4:187605200-187609000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr4:187605400-187607000	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr4:187605400-187607000	Flanking Active TSS	A549	lung
21	chr4:187605400-187607000	Genic enhancers	HMEC	breast
22	chr4:187605400-187607400	Enhancers	Brain Germinal Matrix	brain
23	chr4:187605400-187607800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr4:187605400-187608200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:187605400-187608200	Enhancers	Stomach Mucosa	stomach
26	chr4:187605400-187608800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr4:187605600-187609000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:187605800-187608400	Enhancers	HSMMtube	muscle
29	chr4:187605800-187611200	Enhancers	Rectal Smooth Muscle	rectum
30	chr4:187605800-187614400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr4:187606000-187607200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr4:187606000-187607400	Enhancers	Placenta Amnion	Placenta Amnion
33	chr4:187606000-187608000	Enhancers	Fetal Intestine Large	intestine
34	chr4:187606000-187608000	Enhancers	Small Intestine	intestine
35	chr4:187606000-187608600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:187606000-187608600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr4:187606000-187608800	Enhancers	NHLF	lung
38	chr4:187606000-187609000	Enhancers	Fetal Kidney	kidney
39	chr4:187606000-187610000	Enhancers	NHDF-Ad	bronchial
40	chr4:187606000-187610800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:187606000-187610800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:187606000-187611800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:187606000-187612000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr4:187606200-187608000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr4:187606200-187608000	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr4:187606200-187608000	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr4:187606200-187608200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:187606200-187608200	Enhancers	Fetal Intestine Small	intestine
49	chr4:187606200-187609400	Weak transcription	Pancreas	Pancrea
50	chr4:187606200-187610800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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