Variant report

Variant	rs35085316
Chromosome Location	chr3:120318273-120318274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:120317106-120323167	K562	blood:	n/a	n/a
2	JUN	chr3:120318190-120318390	HepG2	liver:	n/a	chr3:120318230-120318243
3	JUND	chr3:120318056-120318408	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:120317887-120319098	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:120317919-120318503	A549	lung:	n/a	n/a
6	EP300	chr3:120317993-120322832	SK-N-SH	brain:	n/a	chr3:120319021-120319029
7	POLR2A	chr3:120318190-120318575	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr3:120318089-120318570	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:120318272-120318322	AG04450	lung:	fetal
2	chr3:120318272-120318322	SK-N-SH_RA	brain:	n/a
3	chr3:120318272-120318322	GM12878	blood:	n/a
4	chr3:120318272-120318322	HNPCEpiC	eye:	n/a
5	chr3:120318272-120318322	IMR90	lung:	fetal
6	chr3:120318272-120318322	Jurkat	blood:	n/a
7	chr3:120318272-120318322	Hela-S3	cervix:	n/a
8	chr3:120318272-120318322	AG09309	skin:	n/a
9	chr3:120318272-120318322	AoSMC	blood vessel:	n/a
10	chr3:120318272-120318322	HEEpiC	esophagus:	n/a
11	chr3:120318272-120318322	RPTEC	kidney:	n/a
12	chr3:120318272-120318322	K562	blood:	n/a
13	chr3:120318272-120318322	NHBE	bronchial:	n/a
14	chr3:120318272-120318322	HRPEpiC	eye:	n/a
15	chr3:120318272-120318322	GM19239	blood:	n/a
16	chr3:120318272-120318322	GM12892	blood:	n/a
17	chr3:120318272-120318322	A549	lung:	n/a
18	chr3:120318272-120318322	HL-60	blood:	n/a
19	chr3:120318272-120318322	NT2-D1	testis:	n/a
20	chr3:120318272-120318322	HRCEpiC	kidney:	n/a
21	chr3:120318272-120318322	NB4	blood:	n/a
22	chr3:120318272-120318322	CMK	blood:	n/a
23	chr3:120318272-120318322	HRE	kidney:	n/a
24	chr3:120318272-120318322	SK-N-MC	brain:	n/a
25	chr3:120318272-120318322	HMEC	breast:	n/a
26	chr3:120318272-120318322	GM06990	blood:	n/a
27	chr3:120318272-120318322	BJ	skin:	n/a
28	chr3:120318272-120318322	SKMC	muscle:	n/a
29	chr3:120318272-120318322	HAEpiC	amniotic membrane:	n/a
30	chr3:120318272-120318322	MCF-7	breast:	n/a
31	chr3:120318272-120318322	AG10803	skin:	n/a
32	chr3:120318272-120318322	NH-A	brain:	n/a
33	chr3:120318272-120318322	H1-hESC	embryonic stem cell:	embryo
34	chr3:120318272-120318322	GM12891	blood:	n/a
35	chr3:120318272-120318322	SAEC	small airway:	n/a
36	chr3:120318272-120318322	HCT-116	colon:	n/a
37	chr3:120318272-120318322	AG09319	gingival:	n/a
38	chr3:120318272-120318322	T-47D	breast:	n/a
39	chr3:120318272-120318322	BE2_C	brain:	n/a
40	chr3:120318272-120318322	NHDF-neo	bronchial:	n/a
41	chr3:120318272-120318322	HIPEpiC	eye:	n/a
42	chr3:120318272-120318322	PANC-1	pancreas:	n/a
43	chr3:120318272-120318322	HUVEC	blood vessel:	n/a
44	chr3:120318272-120318322	ProgFib	skin:	n/a
45	chr3:120318272-120318322	HPAEpiC	pulmonary alveolar:	n/a
46	chr3:120318272-120318322	HepG2	liver:	n/a
47	chr3:120318272-120318322	U87	brain:	n/a
48	chr3:120318272-120318322	ovcar-3	ovarian:	n/a
49	chr3:120318272-120318322	SK-N-SH	brain:	n/a
50	chr3:120318272-120318322	Hepatocyte	liver:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120315040..120318401-chr3:120459431..120463263,5	MCF-7	breast:

No data

Variant related genes	Relation type
NDUFB4	TF binding region
NDUFB4	CpG island
ENSG00000153767	Chromatin interaction
ENSG00000144840	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12635956	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1465837	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1583654	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831523	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17140281	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17140284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34438738	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34924588	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72625410	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72625411	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72625413	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72625414	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72625415	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72625416	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626272	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv508238	chr3:120248574-120329424	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	esv3373301	chr3:120273762-120421260	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
8	nsv877377	chr3:120287683-120426750	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	esv3464294	chr3:120303062-120420810	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	esv3464295	chr3:120303062-120420810	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120315800-120320200	Weak transcription	Pancreas	Pancrea
2	chr3:120315800-120323600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:120315800-120337200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:120316200-120318600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:120316200-120318800	Enhancers	Stomach Mucosa	stomach
6	chr3:120316200-120323000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:120316200-120323800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:120316200-120335200	Weak transcription	Esophagus	oesophagus
9	chr3:120316400-120318400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:120316400-120318800	Genic enhancers	Fetal Lung	lung
11	chr3:120316400-120319800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:120316400-120320000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:120316600-120318400	Genic enhancers	Liver	Liver
14	chr3:120316600-120318400	Genic enhancers	Fetal Brain Male	brain
15	chr3:120316600-120318600	Strong transcription	Fetal Muscle Trunk	muscle
16	chr3:120316600-120318800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:120316600-120318800	Strong transcription	Fetal Muscle Leg	muscle
18	chr3:120316600-120318800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
19	chr3:120316600-120319000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:120316600-120319200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr3:120316600-120321800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:120316600-120322200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:120316600-120322200	Strong transcription	HSMM	muscle
24	chr3:120316600-120322400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr3:120316600-120323600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:120316800-120318400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:120316800-120318400	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr3:120316800-120318600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:120316800-120318600	Genic enhancers	Ovary	ovary
30	chr3:120316800-120318600	Genic enhancers	Dnd41	blood
31	chr3:120316800-120318600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
32	chr3:120316800-120318800	Genic enhancers	Brain Substantia Nigra	brain
33	chr3:120316800-120318800	Genic enhancers	Rectal Mucosa Donor 31	rectum
34	chr3:120316800-120318800	Genic enhancers	Stomach Smooth Muscle	stomach
35	chr3:120316800-120319000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:120316800-120319000	Genic enhancers	Primary T cells from cord blood	blood
37	chr3:120316800-120319000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr3:120316800-120319000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:120316800-120319000	Strong transcription	A549	lung
40	chr3:120316800-120319200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:120316800-120319200	Genic enhancers	Colon Smooth Muscle	Colon
42	chr3:120316800-120319600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr3:120316800-120319600	Genic enhancers	Duodenum Mucosa	Duodenum
44	chr3:120316800-120319800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
45	chr3:120316800-120319800	Strong transcription	NHDF-Ad	bronchial
46	chr3:120316800-120320600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:120316800-120320800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr3:120316800-120321800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:120316800-120321800	Strong transcription	Placenta	Placenta
50	chr3:120316800-120322000	Strong transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links