Variant report

Variant	rs9303285
Chromosome Location	chr17:38500914-38500915
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	SIN3AK20	chr17:38500659-38500995	A549	lung:	n/a	n/a
2	ZEB1	chr17:38500572-38502778	HepG2	liver:	n/a	n/a
3	RUNX3	chr17:38500744-38501538	GM12878	blood:	n/a	n/a
4	EGR1	chr17:38500816-38501050	K562	blood:	n/a	chr17:38500971-38500985 chr17:38500971-38500982 chr17:38500972-38500982 chr17:38500970-38500984 chr17:38500970-38500983 chr17:38500970-38500983 chr17:38500972-38500982 chr17:38500973-38500982
5	POU2F2	chr17:38500754-38501179	GM12878	blood:	n/a	n/a
6	TCF12	chr17:38500638-38502511	A549	lung:	n/a	chr17:38501639-38501646
7	POLR2A	chr17:38500736-38501645	U87	brain:	n/a	n/a
8	RCOR1	chr17:38500896-38500935	HepG2	liver:	n/a	n/a
9	ZBTB7A	chr17:38500512-38502170	ECC-1	luminal epithelium:	n/a	chr17:38501670-38501678
10	MXI1	chr17:38496997-38502710	SK-N-SH	brain:	n/a	chr17:38502219-38502234
11	POLR2A	chr17:38499249-38501511	MCF-7	breast:	n/a	n/a
12	UBTF	chr17:38500840-38501027	K562	blood:	n/a	n/a
13	EGR1	chr17:38500883-38501024	GM12878	blood:	n/a	chr17:38500971-38500985 chr17:38500971-38500982 chr17:38500972-38500982 chr17:38500970-38500984 chr17:38500970-38500983 chr17:38500970-38500983 chr17:38500972-38500982 chr17:38500973-38500982
14	SPI1	chr17:38500793-38500985	K562	blood:	n/a	chr17:38500887-38500896
15	MXI1	chr17:38500724-38502626	IMR90	lung:	n/a	chr17:38502219-38502234
16	MTA3	chr17:38500575-38501518	GM12878	blood:	n/a	n/a
17	POLR2A	chr17:38500732-38500936	K562	blood:	n/a	n/a
18	POLR2A	chr17:38500423-38502767	HUVEC	blood vessel:	n/a	n/a
19	MAZ	chr17:38497178-38503127	IMR90	lung:	n/a	chr17:38500068-38500078 chr17:38498131-38498141 chr17:38501440-38501451 chr17:38501442-38501449 chr17:38499523-38499533 chr17:38501801-38501811 chr17:38501664-38501674 chr17:38501441-38501450 chr17:38501440-38501450
20	MAX	chr17:38500707-38502487	A549	lung:	n/a	chr17:38501439-38501449 chr17:38501440-38501451 chr17:38501442-38501449 chr17:38501801-38501811 chr17:38501664-38501674 chr17:38501441-38501450 chr17:38501440-38501450
21	SPI1	chr17:38500707-38501071	GM12891	blood:	n/a	chr17:38500887-38500896
22	CHD1	chr17:38496449-38502844	IMR90	lung:	n/a	chr17:38502765-38502775 chr17:38500190-38500200
23	POLR2A	chr17:38500736-38501653	U87	brain:	n/a	n/a
24	NR2F2	chr17:38500566-38501121	K562	blood:	n/a	n/a
25	ZBTB7A	chr17:38500778-38502245	ECC-1	luminal epithelium:	n/a	chr17:38501670-38501678
26	EGR1	chr17:38500750-38501109	K562	blood:	n/a	chr17:38500971-38500985 chr17:38500971-38500982 chr17:38500972-38500982 chr17:38500970-38500984 chr17:38500970-38500983 chr17:38500970-38500983 chr17:38500972-38500982 chr17:38500973-38500982
27	POLR2A	chr17:38500673-38502305	K562	blood:	n/a	n/a
28	BCL3	chr17:38500411-38501045	A549	lung:	n/a	n/a
29	POU2F2	chr17:38500788-38501144	GM12891	blood:	n/a	n/a
30	POLR2A	chr17:38495892-38502181	IMR90	lung:	n/a	n/a
31	POLR2A	chr17:38500826-38502459	HepG2	liver:	n/a	n/a
32	SPI1	chr17:38500708-38501065	GM12878	blood:	n/a	chr17:38500887-38500896
33	POLR2A	chr17:38500526-38502234	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38472788..38480698-chr17:38493295..38509406,39	K562	blood:
2	chr17:38464338..38472007-chr17:38495904..38503617,17	K562	blood:
3	chr17:38275824..38279709-chr17:38496937..38502326,5	K562	blood:
4	chr17:38458898..38461237-chr17:38499745..38502287,2	K562	blood:

Variant related genes	Relation type
RARA	TF binding region
ENSG00000265666	TF binding region
ENSG00000188895	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000270145	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11078939	0.84[EUR][1000 genomes]
rs11078940	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs12051734	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12103711	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12946680	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13706	0.81[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16965687	0.83[GIH][hapmap];0.94[TSI][hapmap]
rs1807273	0.83[ASN][1000 genomes]
rs2077464	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2120200	0.81[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.91[ASN][1000 genomes]
rs2280400	0.83[TSI][hapmap]
rs28537537	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs35286757	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36030243	0.81[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.91[ASN][1000 genomes]
rs4077125	1.00[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs4134994	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4566234	0.93[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs55656553	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55835834	0.82[EUR][1000 genomes]
rs57179137	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59018914	0.82[EUR][1000 genomes]
rs59406133	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59490243	0.91[EUR][1000 genomes]
rs6503539	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7217852	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72836640	0.82[EUR][1000 genomes]
rs7359537	0.83[GIH][hapmap];0.94[TSI][hapmap]
rs8066144	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs8078226	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8080931	0.84[EUR][1000 genomes]
rs9303286	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9891694	0.91[EUR][1000 genomes]
rs9891718	0.82[EUR][1000 genomes]
rs9892946	1.00[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs9893520	0.83[GIH][hapmap];0.94[TSI][hapmap]
rs9894625	0.82[ASN][1000 genomes]
rs9895163	0.84[EUR][1000 genomes]
rs9896312	0.83[ASN][1000 genomes]
rs9904021	1.00[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs9904270	0.81[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9908034	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9910197	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9910788	0.83[AMR][1000 genomes]
rs9911840	0.84[EUR][1000 genomes]
rs9912082	0.84[EUR][1000 genomes]
rs9916460	0.83[GIH][hapmap];0.94[TSI][hapmap]
rs9916782	0.83[GIH][hapmap];0.93[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058194	chr17:38457226-38502453	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1057471	chr17:38467043-38502453	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv1058540	chr17:38467043-38515087	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 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	chr17:38497000-38502400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr17:38497400-38502000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr17:38497400-38502200	Active TSS	Fetal Kidney	kidney
4	chr17:38497600-38501000	Active TSS	HSMM	muscle
5	chr17:38497600-38501600	Active TSS	Small Intestine	intestine
6	chr17:38497600-38502000	Active TSS	HSMMtube	muscle
7	chr17:38497600-38502200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
8	chr17:38498000-38508000	Weak transcription	Dnd41	blood
9	chr17:38498200-38507200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr17:38498400-38501200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr17:38498400-38502400	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr17:38498600-38502400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr17:38498600-38502600	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr17:38498600-38502600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr17:38498600-38503000	Flanking Active TSS	Fetal Muscle Trunk	muscle
16	chr17:38498600-38505800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr17:38498800-38501000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr17:38498800-38501400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr17:38498800-38502400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr17:38498800-38502400	Flanking Active TSS	Osteobl	bone
21	chr17:38498800-38502600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr17:38498800-38502600	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr17:38498800-38502600	Flanking Active TSS	Fetal Brain Female	brain
24	chr17:38498800-38502600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr17:38499000-38501000	Flanking Active TSS	Brain Angular Gyrus	brain
26	chr17:38499000-38501400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
27	chr17:38499000-38501400	Flanking Active TSS	Colon Smooth Muscle	Colon
28	chr17:38499000-38502400	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr17:38499000-38502400	Flanking Active TSS	NH-A	brain
30	chr17:38499000-38502600	Flanking Active TSS	HUVEC	blood vessel
31	chr17:38499000-38502800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr17:38499000-38504000	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr17:38499200-38501000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr17:38499200-38501200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:38499200-38501200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr17:38499200-38501400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:38499200-38501400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr17:38499200-38501600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr17:38499400-38501000	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr17:38499400-38501200	Enhancers	NHEK	skin
41	chr17:38499400-38501400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
42	chr17:38499400-38501400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr17:38499400-38501400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr17:38499400-38501400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
45	chr17:38499400-38501400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr17:38499400-38501400	Flanking Active TSS	Fetal Lung	lung
47	chr17:38499400-38501400	Flanking Active TSS	HepG2	liver
48	chr17:38499400-38502400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr17:38499400-38502400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr17:38499400-38502400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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