Variant report

Variant	rs1713902
Chromosome Location	chr4:122302135-122302136
allele	G/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	RAD21	chr4:122301574-122302445	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr4:122301008-122302583	H1-hESC	embryonic stem cell:	n/a	chr4:122302254-122302265 chr4:122301760-122301775 chr4:122302330-122302337
3	E2F6	chr4:122301392-122302504	H1-hESC	embryonic stem cell:	n/a	chr4:122302254-122302265 chr4:122301760-122301775 chr4:122302330-122302337
4	CEBPB	chr4:122302127-122302599	H1-hESC	embryonic stem cell:	n/a	chr4:122302415-122302426
5	ZNF263	chr4:122301143-122302406	HEK293-T-REx	kidney:	n/a	n/a
6	POLR2A	chr4:122301253-122302809	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr4:122302085-122302312	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr4:122301364-122302467	H1-hESC	embryonic stem cell:	n/a	n/a
9	SIN3A	chr4:122301572-122302334	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr4:122301226-122302366	H1-hESC	embryonic stem cell:	n/a	n/a
11	MYC	chr4:122301064-122302542	MCF10A-Er-Src	breast:	n/a	n/a
12	KAP1	chr4:122301277-122302360	HEK293	kidney:	n/a	n/a
13	POLR2A	chr4:122302027-122302290	H1-hESC	embryonic stem cell:	n/a	n/a
14	E2F6	chr4:122301833-122302471	A549	lung:	n/a	chr4:122302254-122302265 chr4:122302330-122302337
15	MYC	chr4:122300628-122302396	MCF10A-Er-Src	breast:	n/a	chr4:122300983-122300993
16	MYC	chr4:122302091-122302532	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr4:122301529-122302370	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr4:122301690-122302872	MCF10A-Er-Src	breast:	n/a	n/a
19	USF2	chr4:122301977-122302159	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr4:122301457-122302415	A549	lung:	n/a	n/a
21	FOXP2	chr4:122301976-122302442	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr4:122301030-122302853	MCF10A-Er-Src	breast:	n/a	n/a
23	BACH1	chr4:122302125-122302144	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr4:122301415-122302499	H1-hESC	embryonic stem cell:	n/a	n/a
25	E2F6	chr4:122302089-122302372	K562	blood:	n/a	chr4:122302254-122302265 chr4:122302330-122302337
26	TBP	chr4:122301561-122302420	H1-hESC	embryonic stem cell:	n/a	n/a
27	SETDB1	chr4:122301858-122302418	U2OS	brain:	n/a	n/a
28	FOXP2	chr4:122302094-122302323	SK-N-MC	brain:	n/a	n/a
29	E2F4	chr4:122301489-122302471	MCF10A-Er-Src	breast:	n/a	chr4:122302254-122302265 chr4:122301760-122301775 chr4:122302330-122302337
30	TAF1	chr4:122301424-122302272	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr4:122301875-122302369	A549	lung:	n/a	n/a
32	RAD21	chr4:122302036-122302504	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr4:122301513-122302468	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr4:122301914-122302423	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
QRFPR	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12642360	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1513712	0.82[ASN][1000 genomes]
rs2013332	0.96[ASN][1000 genomes]
rs506955	0.96[ASN][1000 genomes]
rs56031223	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6534267	0.93[ASN][1000 genomes]
rs6534268	0.93[ASN][1000 genomes]
rs6828201	0.93[ASN][1000 genomes]
rs9759756	0.82[ASN][1000 genomes]
rs9760672	0.82[ASN][1000 genomes]
rs9761531	0.82[ASN][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	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1009395	chr4:121841442-122557363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv537235	chr4:121841442-122557363	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv879859	chr4:121892490-122438312	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers 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 target site	30 gene(s)	inside rSNPs	diseases
6	nsv508308	chr4:122278897-122312719	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122300200-122302800	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr4:122300600-122302200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:122300800-122302600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr4:122301000-122302200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr4:122301000-122302200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr4:122301000-122302400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
7	chr4:122301000-122302400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr4:122301000-122302400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr4:122301000-122302600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr4:122301000-122302600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
11	chr4:122301000-122302600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr4:122301200-122302400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:122301200-122302400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:122301200-122302400	Bivalent/Poised TSS	Fetal Lung	lung
15	chr4:122301200-122302400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
16	chr4:122301200-122302400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
17	chr4:122301400-122302200	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:122301400-122302200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:122301400-122302200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
20	chr4:122301400-122302200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:122301400-122302200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
22	chr4:122301400-122302200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
23	chr4:122301400-122302200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
24	chr4:122301400-122302400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:122301400-122302400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:122301400-122302400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:122301400-122302400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:122301400-122302400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
29	chr4:122301400-122302400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:122301400-122302400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:122301400-122302400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:122301400-122302400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:122301400-122302400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:122301400-122302400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:122301400-122302400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:122301400-122302400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:122301400-122302400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
38	chr4:122301400-122302400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
39	chr4:122301400-122302400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:122301400-122302400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
41	chr4:122301400-122302400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
42	chr4:122301400-122302400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
43	chr4:122301400-122302400	Bivalent/Poised TSS	Fetal Kidney	kidney
44	chr4:122301400-122302400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
45	chr4:122301400-122302400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
46	chr4:122301400-122302400	Enhancers	Spleen	Spleen
47	chr4:122301600-122302200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr4:122301600-122302200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
49	chr4:122301600-122302200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr4:122301600-122302200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links