Variant report

Variant	rs3827770
Chromosome Location	chr4:102130615-102130616
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:102127770..102129631-chr4:102130414..102132314,2	MCF-7	breast:
2	chr4:102129139..102132021-chr4:102226843..102229507,2	MCF-7	breast:
3	chr4:102129760..102133881-chr4:102266334..102270307,6	MCF-7	breast:
4	chr4:102116031..102123578-chr4:102130356..102136503,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138814	Chromatin interaction
ENSG00000254531	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10005338	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10018021	0.82[EUR][1000 genomes]
rs10025780	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10030389	0.81[EUR][1000 genomes]
rs10050301	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10516471	0.82[EUR][1000 genomes]
rs13103902	0.81[EUR][1000 genomes]
rs13111186	0.81[EUR][1000 genomes]
rs13112866	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13118966	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13125501	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13128841	0.81[EUR][1000 genomes]
rs13135924	0.81[EUR][1000 genomes]
rs13142024	0.81[EUR][1000 genomes]
rs2048072	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2135611	0.81[EUR][1000 genomes]
rs2174680	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3804361	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3804368	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3811063	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4590038	0.81[EUR][1000 genomes]
rs4698912	0.81[EUR][1000 genomes]
rs4698913	0.81[EUR][1000 genomes]
rs4699106	0.81[EUR][1000 genomes]
rs4699116	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4699127	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7677550	0.81[EUR][1000 genomes]
rs950177	0.83[EUR][1000 genomes]
rs9884638	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9995338	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102113800-102131800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr4:102118000-102132600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:102120000-102131400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:102121800-102131200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:102121800-102132600	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:102122000-102132400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:102123200-102131400	Weak transcription	Aorta	Aorta
8	chr4:102123200-102131600	Weak transcription	Small Intestine	intestine
9	chr4:102123200-102132200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:102123200-102132200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:102123200-102132200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:102123200-102132400	Weak transcription	NHEK	skin
13	chr4:102123200-102133400	Weak transcription	Psoas Muscle	Psoas
14	chr4:102123200-102133400	Weak transcription	Right Atrium	heart
15	chr4:102123400-102132800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr4:102124200-102132800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:102127200-102132200	Weak transcription	HSMM	muscle
18	chr4:102127400-102132000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:102127400-102132000	Weak transcription	NH-A	brain
20	chr4:102127400-102132200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr4:102127400-102132200	Weak transcription	HMEC	breast
22	chr4:102127400-102132200	Weak transcription	NHDF-Ad	bronchial
23	chr4:102127400-102132600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:102127800-102131600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr4:102127800-102131800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:102127800-102132200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:102127800-102132200	Weak transcription	Osteobl	bone
28	chr4:102128000-102138200	Weak transcription	Primary B cells from cord blood	blood
29	chr4:102128200-102131400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:102128200-102132000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr4:102129000-102131200	Enhancers	A549	lung
32	chr4:102129000-102140400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr4:102129600-102132600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:102129600-102135600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:102129600-102138600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr4:102130600-102132200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links