Variant report

Variant	rs17421743
Chromosome Location	chr2:38825407-38825408
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr2:38825264-38825481	SH-SY5Y	brain:	n/a	chr2:38825369-38825385
2	POLR2A	chr2:38825324-38828171	HepG2	liver:	n/a	n/a
3	ARID3A	chr2:38825253-38825528	K562	blood:	n/a	n/a
4	RCOR1	chr2:38825322-38825545	K562	blood:	n/a	n/a
5	POLR2A	chr2:38825374-38825560	HepG2	liver:	n/a	n/a
6	SPI1	chr2:38825303-38825679	GM12891	blood:	n/a	chr2:38825342-38825355
7	PML	chr2:38825268-38825911	K562	blood:	n/a	n/a
8	JUND	chr2:38825331-38825697	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:38825253-38825889	K562	blood:	n/a	n/a
10	POLR2A	chr2:38825204-38826182	K562	blood:	n/a	n/a
11	ATF2	chr2:38825289-38825669	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr2:38821640-38832164	K562	blood:	n/a	n/a
13	SPI1	chr2:38825355-38825612	GM12891	blood:	n/a	n/a
14	JUND	chr2:38825341-38825658	K562	blood:	n/a	n/a
15	JUN	chr2:38825356-38825696	HepG2	liver:	n/a	chr2:38825505-38825518
16	GATA2	chr2:38825218-38825551	SH-SY5Y	brain:	n/a	chr2:38825369-38825385
17	KAP1	chr2:38825374-38826435	U2OS	brain:	n/a	n/a
18	POLR2A	chr2:38825282-38829280	K562	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38823060..38827854-chr2:38827983..38831423,11	MCF-7	breast:
2	chr2:38824718..38826820-chr2:38951264..38953232,2	K562	blood:
3	chr2:38819128..38833161-chr2:38974716..38980003,37	K562	blood:
4	chr2:38822893..38825624-chr2:38929270..38931305,2	K562	blood:
5	chr2:38824811..38832919-chr2:38891494..38898299,16	K562	blood:
6	chr2:38824074..38831950-chr2:38975822..38980618,12	MCF-7	breast:
7	chr2:38824026..38825901-chr2:38962946..38965190,2	K562	blood:
8	chr2:38824210..38826669-chr2:38912161..38913673,2	MCF-7	breast:
9	chr2:38820462..38822126-chr2:38823935..38825729,2	MCF-7	breast:
10	chr2:38823862..38826061-chr2:38919360..38922289,2	K562	blood:
11	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
12	chr2:38823625..38826319-chr2:38903588..38906507,3	K562	blood:
13	chr2:38824770..38827325-chr2:38977013..38980268,3	MCF-7	breast:
14	chr2:38821957..38830238-chr2:38965333..38974515,17	K562	blood:
15	chr2:38823851..38826080-chr2:38908814..38911340,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000235586	TF binding region
ENSG00000235586	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000143891	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10495880	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12987111	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990659	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12991911	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs12995222	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12996029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011896	0.91[AFR][1000 genomes]
rs1540436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17421378	0.94[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs17421399	0.80[CEU][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap]
rs17421503	0.94[CEU][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs17421545	0.85[ASN][1000 genomes]
rs17421587	0.82[EUR][1000 genomes]
rs17493321	0.82[JPT][hapmap]
rs17493363	0.88[CEU][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs17493370	0.80[CEU][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs17493419	0.94[CEU][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs17493538	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17493573	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17493594	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17493839	0.84[ASN][1000 genomes]
rs17575960	0.83[CEU][hapmap]
rs17603796	0.80[ASN][1000 genomes]
rs1864828	0.80[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1864829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864830	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213851	0.81[ASN][1000 genomes]
rs34462852	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34533895	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34688430	0.88[ASN][1000 genomes]
rs34821677	0.88[ASN][1000 genomes]
rs35151237	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35219064	0.95[EUR][1000 genomes]
rs35378647	0.88[ASN][1000 genomes]
rs35492507	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35581112	0.91[ASN][1000 genomes]
rs35679136	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35734673	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35869291	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35933789	0.83[AFR][1000 genomes]
rs4268910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4536633	0.88[ASN][1000 genomes]
rs55948796	0.88[ASN][1000 genomes]
rs56208611	0.89[ASN][1000 genomes]
rs56217714	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6704829	0.89[ASN][1000 genomes]
rs6710118	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6722560	0.88[ASN][1000 genomes]
rs6731029	1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs6733848	1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs6745023	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6749343	0.94[EUR][1000 genomes]
rs6750764	0.88[ASN][1000 genomes]
rs67772386	0.82[EUR][1000 genomes]
rs68109027	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs72905846	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs72905865	0.95[ASN][1000 genomes]
rs72907903	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573095	0.80[ASN][1000 genomes]
rs7574556	0.80[CEU][hapmap];0.82[JPT][hapmap]
rs891705	0.90[JPT][hapmap]
rs919698	0.89[CEU][hapmap]
rs934394	0.94[CEU][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs934395	0.94[CEU][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581482	chr2:38799820-38858669	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38781200-38827600	Weak transcription	Esophagus	oesophagus
2	chr2:38783800-38827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:38785000-38827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:38786000-38827600	Weak transcription	Colonic Mucosa	Colon
5	chr2:38798000-38827600	Weak transcription	Spleen	Spleen
6	chr2:38798200-38827600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:38799800-38827800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:38805200-38826400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:38808800-38827000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr2:38808800-38827400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:38808800-38827400	Weak transcription	Pancreas	Pancrea
12	chr2:38809000-38825600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:38809400-38825800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:38809600-38827400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:38810000-38827600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:38813200-38826000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:38813400-38827000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:38814400-38825600	Weak transcription	HUVEC	blood vessel
19	chr2:38815200-38825800	Weak transcription	Fetal Brain Male	brain
20	chr2:38818400-38827600	Weak transcription	Placenta	Placenta
21	chr2:38818800-38825600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr2:38818800-38825600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:38818800-38825600	Weak transcription	HSMM	muscle
24	chr2:38819600-38827400	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr2:38820200-38825600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr2:38820200-38827800	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr2:38821000-38825600	Weak transcription	Brain Anterior Caudate	brain
28	chr2:38821000-38827000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:38821000-38827400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:38822200-38825600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:38822400-38825600	Weak transcription	Adipose Nuclei	Adipose
32	chr2:38822400-38825600	Weak transcription	Right Atrium	heart
33	chr2:38822400-38825600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:38822400-38825600	Weak transcription	HMEC	breast
35	chr2:38822400-38825600	Weak transcription	NHEK	skin
36	chr2:38822400-38826000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:38822400-38827600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:38822400-38828600	Weak transcription	Lung	lung
39	chr2:38822800-38830400	Active TSS	Primary T cells fromperipheralblood	blood
40	chr2:38823200-38827000	Enhancers	Colon Smooth Muscle	Colon
41	chr2:38823400-38825800	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr2:38823600-38825600	Enhancers	HepG2	liver
43	chr2:38823600-38825800	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr2:38823600-38825800	Enhancers	A549	lung
45	chr2:38823800-38826000	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr2:38824000-38827000	Enhancers	Fetal Lung	lung
47	chr2:38824200-38825600	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr2:38824400-38828200	Enhancers	Fetal Heart	heart
49	chr2:38824600-38826800	Weak transcription	Fetal Brain Female	brain
50	chr2:38824600-38827400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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