Variant report

Variant	rs35624684
Chromosome Location	chr17:46658475-46658476
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	SUZ12	chr17:46657913-46660550	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr17:46658373-46660633	K562	blood:	n/a	n/a
3	SUZ12	chr17:46653107-46661081	NT2-D1	testis:	n/a	n/a
4	SPI1	chr17:46658219-46658512	GM12891	blood:	n/a	chr17:46658298-46658307
5	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
6	TCF7L2	chr17:46657383-46658749	HEK293	kidney:	n/a	chr17:46657965-46657981 chr17:46657966-46657980 chr17:46657967-46657977 chr17:46657968-46657977 chr17:46657965-46657981 chr17:46657969-46657978
7	CHD1	chr17:46655927-46662288	IMR90	lung:	n/a	chr17:46657663-46657673 chr17:46660648-46660658
8	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46459433..46462163-chr17:46658202..46660838,2	K562	blood:
2	chr17:46525263..46527446-chr17:46657806..46659592,2	K562	blood:
3	chr17:46652243..46654179-chr17:46657727..46659805,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HOXB4-1	chr17:46656992-46659621	ENSG00000257178.1

Variant related genes	Relation type
HOXB3	TF binding region
MIR10A	TF binding region
HOXB4	TF binding region
ENSG00000120093	Chromatin interaction
ENSG00000200538	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1042818	0.83[AMR][1000 genomes]
rs1042822	0.83[AMR][1000 genomes]
rs1062037	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1123630	0.83[EUR][1000 genomes]
rs12951076	0.85[AMR][1000 genomes]
rs2229302	0.83[AMR][1000 genomes]
rs34490194	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34527992	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34822124	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35825473	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4793589	0.83[EUR][1000 genomes]
rs4793937	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4793938	0.83[EUR][1000 genomes]
rs4793939	0.83[EUR][1000 genomes]
rs4793943	0.83[EUR][1000 genomes]
rs56128659	0.85[AMR][1000 genomes]
rs66459980	0.83[EUR][1000 genomes]
rs67412921	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs872760	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
2	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases
3	nsv908577	chr17:46584900-46704536	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	343 gene(s)	inside rSNPs	diseases
4	nsv908578	chr17:46592413-46698710	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
5	nsv908579	chr17:46592413-46727289	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
6	nsv532113	chr17:46598247-47588570	Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	453 gene(s)	inside rSNPs	diseases
7	esv2758459	chr17:46602673-46836837	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
8	esv2758694	chr17:46602673-46836837	Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
9	nsv908580	chr17:46609103-46698710	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
10	nsv908581	chr17:46610646-46735520	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
11	nsv575480	chr17:46617019-46684929	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
12	nsv908582	chr17:46617019-46698710	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
13	nsv908583	chr17:46617019-46704536	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
14	nsv833471	chr17:46617787-46783345	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	356 gene(s)	inside rSNPs	diseases
15	nsv908584	chr17:46618926-46735520	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
16	nsv457822	chr17:46620402-46698710	Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
17	nsv575481	chr17:46620402-46698710	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
18	nsv457823	chr17:46620402-46704536	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
19	nsv575482	chr17:46620402-46704536	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
20	nsv457824	chr17:46625519-46693491	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
21	nsv575483	chr17:46625519-46693491	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35624684	HOXB2	cis	Thyroid	GTEx
rs35624684	HOXB-AS1	cis	Whole Blood	GTEx
rs35624684	HOXB2	cis	Adipose Subcutaneous	GTEx
rs35624684	HOXB2	cis	Whole Blood	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46653400-46660400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
2	chr17:46653600-46660200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr17:46656000-46659200	Flanking Active TSS	HUVEC	blood vessel
4	chr17:46656000-46660600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr17:46656000-46661200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:46656600-46658600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr17:46656600-46658600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
8	chr17:46656600-46658600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
9	chr17:46656600-46658800	Weak transcription	Aorta	Aorta
10	chr17:46656600-46659200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr17:46656800-46658600	Active TSS	Colonic Mucosa	Colon
12	chr17:46656800-46658800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
13	chr17:46656800-46658800	Weak transcription	Esophagus	oesophagus
14	chr17:46656800-46659000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
15	chr17:46656800-46659000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr17:46656800-46659000	Weak transcription	Spleen	Spleen
17	chr17:46657000-46658800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr17:46657000-46658800	Active TSS	NHLF	lung
19	chr17:46657000-46659000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
20	chr17:46657000-46659000	Enhancers	GM12878-XiMat	blood
21	chr17:46657400-46658800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
22	chr17:46657400-46658800	Flanking Active TSS	K562	blood
23	chr17:46657400-46659200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
24	chr17:46657600-46658800	Weak transcription	Right Atrium	heart
25	chr17:46657600-46659000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
26	chr17:46657800-46659000	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr17:46657800-46659600	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr17:46657800-46660200	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr17:46658000-46658800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr17:46658000-46658800	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr17:46658000-46658800	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr17:46658000-46659000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr17:46658000-46659000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr17:46658000-46659000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr17:46658000-46659800	Bivalent/Poised TSS	Lung	lung
36	chr17:46658000-46661000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
37	chr17:46658200-46658600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr17:46658200-46658600	Flanking Active TSS	HSMM	muscle
39	chr17:46658200-46658800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr17:46658200-46659000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr17:46658200-46659000	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr17:46658200-46660000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
43	chr17:46658200-46660000	Weak transcription	A549	lung
44	chr17:46658400-46658600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
45	chr17:46658400-46658800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr17:46658400-46658800	Flanking Active TSS	Fetal Kidney	kidney
47	chr17:46658400-46658800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
48	chr17:46658400-46658800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
49	chr17:46658400-46658800	Flanking Active TSS	NHDF-Ad	bronchial
50	chr17:46658400-46659000	Flanking Bivalent TSS/Enh	Fetal Lung	lung

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