Variant report

Variant	rs3759935
Chromosome Location	chr16:81041928-81041929
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:81039828-81042424	MCF10A-Er-Src	breast:	n/a	n/a
2	MAX	chr16:81041854-81042190	K562	blood:	n/a	n/a
3	POLR2A	chr16:81039833-81042011	GM12892	blood:	n/a	n/a
4	JUND	chr16:81039279-81042090	SK-N-SH	brain:	n/a	chr16:81041079-81041088
5	WRNIP1	chr16:81040276-81041959	GM12878	blood:	n/a	n/a
6	YY1	chr16:81041879-81042119	K562	blood:	n/a	n/a
7	POLR2A	chr16:81039798-81042062	GM12878	blood:	n/a	n/a
8	POLR2A	chr16:81039886-81042074	HepG2	liver:	n/a	n/a
9	YY1	chr16:81041801-81042164	GM12892	blood:	n/a	n/a
10	MXI1	chr16:81039145-81042276	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr16:81039896-81042204	K562	blood:	n/a	n/a
12	GTF3C2	chr16:81040923-81041948	Hela-S3	cervix:	n/a	n/a
13	EGR1	chr16:81039781-81041982	HCT-116	colon:	n/a	chr16:81041050-81041063 chr16:81040794-81040804 chr16:81041050-81041063 chr16:81040073-81040087 chr16:81041049-81041064 chr16:81041050-81041063 chr16:81040519-81040528
14	HCFC1	chr16:81039075-81042051	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr16:81040075-81042015	HUVEC	blood vessel:	n/a	n/a
16	HEY1	chr16:81039788-81042481	K562	blood:	n/a	chr16:81041078-81041087 chr16:81041080-81041089 chr16:81040141-81040156
17	POLR2A	chr16:81041646-81041970	HUVEC	blood vessel:	n/a	n/a
18	CHD1	chr16:81039191-81042059	IMR90	lung:	n/a	chr16:81041086-81041096
19	SREBP1	chr16:81040019-81042204	GM12878	blood:	n/a	n/a
20	POLR2A	chr16:81039866-81042151	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:81038105..81044923-chr16:81066300..81070952,14	MCF-7	breast:
2	chr16:81037151..81044642-chr16:81065528..81070966,16	K562	blood:
3	chr16:81028135..81034571-chr16:81035246..81044200,13	K562	blood:
4	chr16:81041195..81043278-chr16:81298968..81300787,2	MCF-7	breast:
5	chr16:81041193..81042878-chr16:81061332..81063223,2	MCF-7	breast:
6	chr16:81037996..81043724-chr16:81066407..81071400,11	MCF-7	breast:
7	chr16:81038376..81042418-chr16:81108432..81111584,4	K562	blood:
8	chr16:81037094..81043910-chr16:81050858..81058489,11	MCF-7	breast:
9	chr16:81041089..81043936-chr16:81047527..81050670,4	MCF-7	breast:
10	chr16:81038376..81043277-chr16:81108432..81112403,6	K562	blood:
11	chr16:81037151..81042784-chr16:81066438..81073797,14	K562	blood:
12	chr16:81006720..81008991-chr16:81041065..81043268,2	MCF-7	breast:
13	chr16:81041904..81044341-chr16:81779163..81781549,2	MCF-7	breast:
14	chr16:81039722..81044457-chr16:81106699..81112118,5	MCF-7	breast:

Variant related genes	Relation type
CMC2	TF binding region
ENSG00000103121	Chromatin interaction
ENSG00000245059	Chromatin interaction
ENSG00000166454	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000260213	Chromatin interaction
ENSG00000166451	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12932976	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35496593	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1065258	chr16:80887483-81081768	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1058045	chr16:80918138-81048242	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1064164	chr16:80918138-81126967	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv542991	chr16:80918138-81126967	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv573338	chr16:81020393-81106944	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81037800-81042000	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr16:81037800-81042400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr16:81038200-81042000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr16:81038200-81042400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr16:81038400-81042000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr16:81038400-81042200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr16:81038400-81042200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr16:81038800-81042000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr16:81038800-81042200	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr16:81038800-81042200	Active TSS	A549	lung
11	chr16:81038800-81042400	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr16:81039400-81042000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr16:81039400-81042200	Active TSS	Colonic Mucosa	Colon
14	chr16:81039400-81042400	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr16:81039400-81042400	Active TSS	NHLF	lung
16	chr16:81039600-81042000	Active TSS	H1 Cell Line	embryonic stem cell
17	chr16:81039600-81042000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr16:81039600-81042000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr16:81039600-81042000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr16:81039600-81042000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr16:81039600-81042000	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr16:81039600-81042000	Active TSS	Brain Angular Gyrus	brain
23	chr16:81039600-81042000	Active TSS	Brain Substantia Nigra	brain
24	chr16:81039600-81042000	Active TSS	Esophagus	oesophagus
25	chr16:81039600-81042000	Active TSS	Fetal Intestine Small	intestine
26	chr16:81039600-81042000	Active TSS	Pancreas	Pancrea
27	chr16:81039600-81042000	Active TSS	Right Atrium	heart
28	chr16:81039600-81042000	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr16:81039600-81042000	Active TSS	GM12878-XiMat	blood
30	chr16:81039600-81042200	Active TSS	H9 Cell Line	embryonic stem cell
31	chr16:81039600-81042200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr16:81039600-81042200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr16:81039600-81042200	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr16:81039600-81042200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr16:81039600-81042200	Active TSS	Fetal Intestine Large	intestine
36	chr16:81039600-81042200	Active TSS	Fetal Stomach	stomach
37	chr16:81039600-81042200	Active TSS	NHDF-Ad	bronchial
38	chr16:81039600-81042400	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr16:81039600-81042400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr16:81039600-81042400	Active TSS	Brain Germinal Matrix	brain
41	chr16:81039600-81042400	Active TSS	Brain Hippocampus Middle	brain
42	chr16:81039600-81042400	Active TSS	HSMM	muscle
43	chr16:81039800-81042000	Active TSS	Aorta	Aorta
44	chr16:81039800-81042000	Active TSS	Brain Anterior Caudate	brain
45	chr16:81039800-81042000	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr16:81039800-81042000	Active TSS	HSMMtube	muscle
47	chr16:81039800-81042000	Active TSS	Osteobl	bone
48	chr16:81039800-81042200	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr16:81039800-81042200	Active TSS	Colon Smooth Muscle	Colon
50	chr16:81039800-81042200	Active TSS	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links