Variant report

Variant	rs17839573
Chromosome Location	chr16:31211432-31211433
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:59)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:59 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:31205085-31214379	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr16:31211191-31211432	HCT-116	colon:	n/a	n/a
3	POLR2A	chr16:31210590-31211701	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr16:31211231-31211432	H1-hESC	embryonic stem cell:	n/a	n/a
5	BCL3	chr16:31210519-31211465	A549	lung:	n/a	n/a
6	POLR2A	chr16:31196099-31214010	K562	blood:	n/a	n/a
7	POLR2A	chr16:31210577-31211555	GM18505	blood:	n/a	n/a
8	POLR2A	chr16:31207436-31211574	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr16:31196354-31214629	GM12891	blood:	n/a	n/a
10	POLR2A	chr16:31196046-31214408	GM12892	blood:	n/a	n/a
11	POLR2A	chr16:31196323-31214177	GM12892	blood:	n/a	n/a
12	POLR2A	chr16:31196746-31214240	GM12891	blood:	n/a	n/a
13	MTA3	chr16:31208186-31211539	GM12878	blood:	n/a	n/a
14	POLR2A	chr16:31203206-31211716	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr16:31209015-31211472	U87	brain:	n/a	n/a
16	POLR2A	chr16:31196474-31211565	HepG2	liver:	n/a	n/a
17	POLR2A	chr16:31205097-31211681	U87	brain:	n/a	n/a
18	POLR2A	chr16:31197288-31214611	GM12891	blood:	n/a	n/a
19	POLR2A	chr16:31208991-31211611	K562	blood:	n/a	n/a
20	POLR2A	chr16:31207313-31211461	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr16:31208541-31211769	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr16:31209043-31211485	GM12878	blood:	n/a	n/a
23	POLR2A	chr16:31200960-31211583	GM12878	blood:	n/a	n/a
24	POLR2A	chr16:31208961-31211731	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr16:31210741-31211623	GM19193	blood:	n/a	n/a
26	MAFK	chr16:31211359-31211661	HepG2	liver:	n/a	n/a
27	POLR2A	chr16:31208494-31211873	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr16:31196345-31214090	GM12892	blood:	n/a	n/a
29	POLR2A	chr16:31196170-31216645	HepG2	liver:	n/a	n/a
30	POLR2A	chr16:31210677-31211504	HepG2	liver:	n/a	n/a
31	HEY1	chr16:31210647-31211449	HepG2	liver:	n/a	n/a
32	POLR2A	chr16:31196205-31214694	GM12891	blood:	n/a	n/a
33	POLR2A	chr16:31208991-31211828	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr16:31208118-31211674	HL-60	blood:	n/a	n/a
35	POLR2A	chr16:31195988-31211763	HepG2	liver:	n/a	n/a
36	POLR2A	chr16:31190296-31214398	PANC-1	pancreas:	n/a	n/a
37	POLR2A	chr16:31210625-31211456	GM12878	blood:	n/a	n/a
38	POLR2A	chr16:31210643-31214383	K562	blood:	n/a	n/a
39	POLR2A	chr16:31190139-31214678	GM12878	blood:	n/a	n/a
40	POLR2A	chr16:31202402-31211470	K562	blood:	n/a	n/a
41	NFATC1	chr16:31207379-31211687	GM12878	blood:	n/a	n/a
42	NFATC1	chr16:31208240-31214097	GM12878	blood:	n/a	chr16:31212456-31212470
43	USF2	chr16:31211320-31211454	HepG2	liver:	n/a	n/a
44	POLR2A	chr16:31210616-31212056	GM12891	blood:	n/a	n/a
45	POLR2A	chr16:31210552-31211691	SK-N-MC	brain:	n/a	n/a
46	POLR2A	chr16:31207374-31211443	MCF-7	breast:	n/a	n/a
47	POLR2A	chr16:31196143-31216629	A549	lung:	n/a	n/a
48	POLR2A	chr16:31195969-31215569	GM12878	blood:	n/a	n/a
49	POLR2A	chr16:31210658-31212085	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr16:31210696-31211561	Hela-S3	cervix:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:31209888..31212033-chr16:31451859..31453870,2	K562	blood:
2	chr16:31210088..31212340-chr16:31394934..31396968,2	MCF-7	breast:
3	chr16:31210690..31213656-chr16:31469495..31472213,2	MCF-7	breast:
4	chr16:31211282..31213179-chr16:31343243..31345626,2	K562	blood:
5	chr16:31210451..31214037-chr16:31224426..31227776,4	MCF-7	breast:
6	chr16:31209517..31212258-chr16:31227042..31229514,2	K562	blood:
7	chr16:31211041..31212980-chr16:31217003..31219469,2	MCF-7	breast:
8	chr16:31127728..31129952-chr16:31209751..31212374,2	K562	blood:
9	chr16:31210307..31213024-chr16:31213312..31215668,2	MCF-7	breast:

No data

Variant related genes	Relation type
C16orf98	TF binding region
ENSG00000140691	Chromatin interaction
ENSG00000260267	Chromatin interaction
ENSG00000177238	Chromatin interaction
ENSG00000262766	Chromatin interaction
ENSG00000103510	Chromatin interaction
ENSG00000169900	Chromatin interaction
ENSG00000103490	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10782003	1.00[EUR][1000 genomes]
rs16956408	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17839571	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55643523	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55651936	1.00[EUR][1000 genomes]
rs55995755	1.00[EUR][1000 genomes]
rs56068718	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58076927	1.00[EUR][1000 genomes]
rs58865641	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59064674	1.00[EUR][1000 genomes]
rs60375074	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60976516	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61086377	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61196325	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61733962	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs68121698	1.00[EUR][1000 genomes]
rs7186737	1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72550895	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73530254	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73530256	1.00[AMR][1000 genomes]
rs73530263	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73530266	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73530269	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73530272	1.00[EUR][1000 genomes]
rs73530280	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73530283	1.00[EUR][1000 genomes]
rs73530293	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73530298	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73532211	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73532214	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73532217	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73532228	1.00[EUR][1000 genomes]
rs73532236	1.00[EUR][1000 genomes]
rs73532241	1.00[EUR][1000 genomes]
rs73532245	1.00[EUR][1000 genomes]
rs73532246	1.00[EUR][1000 genomes]
rs73532249	1.00[EUR][1000 genomes]
rs73532254	1.00[EUR][1000 genomes]
rs74015090	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74015096	1.00[EUR][1000 genomes]
rs9708646	1.00[EUR][1000 genomes]
rs9927298	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
4	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
5	nsv905735	chr16:30890538-31247924	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	264 gene(s)	inside rSNPs	diseases
6	nsv905740	chr16:31066249-31232437	Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
7	nsv905741	chr16:31066249-31247924	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
8	nsv905742	chr16:31102321-31247924	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	188 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31195400-31211600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr16:31195400-31211600	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr16:31195400-31212400	Strong transcription	Fetal Stomach	stomach
4	chr16:31195400-31213000	Weak transcription	Right Atrium	heart
5	chr16:31195600-31211800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr16:31195600-31211800	Strong transcription	Fetal Muscle Trunk	muscle
7	chr16:31195600-31212400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr16:31195600-31212400	Strong transcription	Fetal Brain Female	brain
9	chr16:31195800-31212600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr16:31197200-31211600	Strong transcription	NHDF-Ad	bronchial
11	chr16:31197200-31212600	Strong transcription	Fetal Muscle Leg	muscle
12	chr16:31197600-31212600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr16:31198600-31212600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr16:31198800-31212200	Strong transcription	Skeletal Muscle Male	skeletal muscle
15	chr16:31200800-31213200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr16:31202000-31211600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr16:31202600-31213000	Weak transcription	Psoas Muscle	Psoas
18	chr16:31203800-31212000	Weak transcription	Fetal Heart	heart
19	chr16:31204800-31212400	Weak transcription	Stomach Mucosa	stomach
20	chr16:31205800-31212200	Weak transcription	Small Intestine	intestine
21	chr16:31205800-31214800	Weak transcription	Hela-S3	cervix
22	chr16:31206400-31213200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr16:31207200-31211800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
24	chr16:31207200-31212200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr16:31207400-31212600	Weak transcription	Colon Smooth Muscle	Colon
26	chr16:31207600-31211600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr16:31207600-31211600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr16:31207800-31212800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr16:31208000-31212200	Weak transcription	Esophagus	oesophagus
30	chr16:31208000-31212200	Weak transcription	Spleen	Spleen
31	chr16:31208000-31212400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr16:31208000-31212400	Weak transcription	Fetal Kidney	kidney
33	chr16:31208000-31212400	Weak transcription	Gastric	stomach
34	chr16:31208000-31212400	Weak transcription	Pancreas	Pancrea
35	chr16:31208000-31212400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr16:31208000-31212800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr16:31208000-31212800	Weak transcription	Ovary	ovary
38	chr16:31208000-31212800	Weak transcription	HUVEC	blood vessel
39	chr16:31208000-31213000	Weak transcription	Left Ventricle	heart
40	chr16:31208200-31212400	Weak transcription	Brain Anterior Caudate	brain
41	chr16:31208200-31212400	Weak transcription	Colonic Mucosa	Colon
42	chr16:31208200-31213000	Weak transcription	HSMMtube	muscle
43	chr16:31208400-31212000	Weak transcription	Liver	Liver
44	chr16:31208400-31212200	Weak transcription	HMEC	breast
45	chr16:31208400-31212400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr16:31208400-31212400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr16:31208400-31212600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr16:31208400-31212600	Weak transcription	Fetal Lung	lung
49	chr16:31208400-31212600	Weak transcription	Right Ventricle	heart
50	chr16:31208600-31212400	Weak transcription	H1 Cell Line	embryonic stem cell

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