Variant report

Variant	rs58994962
Chromosome Location	chr1:173831299-173831300
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:178)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:178 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:173830742-173838152	GM18951	blood:	n/a	n/a
2	POLR2A	chr1:173830604-173834319	HL-60	blood:	n/a	n/a
3	POLR2A	chr1:173831251-173832299	Gliobla	brain:	n/a	n/a
4	SP4	chr1:173831059-173831395	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:173829652-173834370	K562	blood:	n/a	n/a
6	PBX3	chr1:173830727-173831588	A549	lung:	n/a	n/a
7	POLR2A	chr1:173828332-173838242	K562	blood:	n/a	n/a
8	PBX3	chr1:173830728-173832741	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr1:173831238-173832410	GM12878	blood:	n/a	n/a
10	CEBPD	chr1:173830788-173832895	K562	blood:	n/a	n/a
11	POLR2A	chr1:173831275-173832049	GM12878	blood:	n/a	n/a
12	ATF3	chr1:173830958-173832035	A549	lung:	n/a	n/a
13	FOSL2	chr1:173830851-173831422	A549	lung:	n/a	n/a
14	SIN3AK20	chr1:173830842-173831439	K562	blood:	n/a	n/a
15	SIN3AK20	chr1:173830744-173831539	A549	lung:	n/a	n/a
16	ATF2	chr1:173830850-173831447	GM12878	blood:	n/a	n/a
17	JUND	chr1:173830922-173831493	A549	lung:	n/a	n/a
18	POLR2A	chr1:173829381-173833686	GM12891	blood:	n/a	n/a
19	POLR2A	chr1:173825088-173838434	K562	blood:	n/a	n/a
20	POU2F2	chr1:173830712-173831456	GM12891	blood:	n/a	n/a
21	POLR2A	chr1:173827997-173836225	HepG2	liver:	n/a	n/a
22	POLR2A	chr1:173830571-173832892	GM12891	blood:	n/a	n/a
23	SIN3AK20	chr1:173830728-173831998	A549	lung:	n/a	n/a
24	NFIC	chr1:173831127-173831411	HepG2	liver:	n/a	n/a
25	POLR2A	chr1:173830687-173832742	Raji	blood:	n/a	n/a
26	CREB1	chr1:173830647-173831538	K562	blood:	n/a	n/a
27	POLR2A	chr1:173829861-173834161	K562	blood:	n/a	n/a
28	POLR2A	chr1:173829985-173833751	GM19193	blood:	n/a	n/a
29	ZBTB33	chr1:173830919-173831482	A549	lung:	n/a	n/a
30	POLR2A	chr1:173824570-173837689	A549	lung:	n/a	n/a
31	FOSL2	chr1:173830806-173831382	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr1:173828233-173834504	GM12892	blood:	n/a	n/a
33	POLR2A	chr1:173830753-173833030	HCT-116	colon:	n/a	n/a
34	RUNX3	chr1:173831046-173831538	GM12878	blood:	n/a	n/a
35	JUND	chr1:173830702-173832980	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr1:173829284-173838362	K562	blood:	n/a	n/a
37	POLR2A	chr1:173829132-173838052	PFSK-1	brain:	n/a	n/a
38	MAZ	chr1:173831272-173831346	HepG2	liver:	n/a	n/a
39	BCLAF1	chr1:173831014-173831571	K562	blood:	n/a	n/a
40	POLR2A	chr1:173829663-173838350	K562	blood:	n/a	n/a
41	SP1	chr1:173831237-173831991	A549	lung:	n/a	n/a
42	POLR2A	chr1:173829737-173838261	PANC-1	pancreas:	n/a	n/a
43	REST	chr1:173830937-173831425	A549	lung:	n/a	n/a
44	POLR2A	chr1:173829767-173838193	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:173829946-173832856	NB4	blood:	n/a	n/a
46	BCLAF1	chr1:173830668-173832603	GM12878	blood:	n/a	chr1:173831994-173832003
47	MTA3	chr1:173830550-173833227	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:173829033-173834330	U87	brain:	n/a	n/a
49	POLR2A	chr1:173829700-173838480	GM18505	blood:	n/a	n/a
50	BCLAF1	chr1:173830767-173831477	K562	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173829871..173833250-chr1:173884943..173888028,3	K562	blood:
2	chr1:173829121..173831364-chr1:173963945..173965806,2	MCF-7	breast:
3	chr1:173829567..173831571-chr1:173900129..173902507,2	K562	blood:
4	chr1:173828767..173831620-chr1:173909948..173912434,2	K562	blood:
5	chr1:173642158..173644054-chr1:173829177..173831512,2	K562	blood:
6	chr1:173789792..173811494-chr1:173827886..173840273,103	K562	blood:
7	chr1:173829761..173831898-chr1:173903649..173905478,2	K562	blood:
8	chr1:173831168..173832165-chr16:1822973..1823541,2	Hela-S3	cervix:
9	chr1:173682439..173685635-chr1:173828531..173832401,4	MCF-7	breast:
10	chr1:173830867..173831834-chr19:41257160..41257671,2	Hela-S3	cervix:
11	chr1:173793576..173795606-chr1:173831172..173833639,2	MCF-7	breast:
12	chr1:173829979..173831869-chr1:173877762..173880722,2	K562	blood:
13	chr1:173789473..173804179-chr1:173828884..173842109,95	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DARS2-1	chr1:173831290-173831426	XLOC_000467
2	lnc-SERPINC1-1	chr1:173827684-173834420	NONHSAT007659

No data

Variant related genes	Relation type
GAS5-AS1	TF binding region
ENSG00000074071	Chromatin interaction
ENSG00000117593	Chromatin interaction
ENSG00000076321	Chromatin interaction
ENSG00000197774	Chromatin interaction
ENSG00000135870	Chromatin interaction
ENSG00000117601	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000120334	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs16846418	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16846433	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16846478	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16846526	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16846546	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16846561	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2065170	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2068871	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2146372	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2227589	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2227592	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2235095	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2759328	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3791021	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3791022	0.86[ASN][1000 genomes]
rs57022387	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61262741	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61649485	0.86[ASN][1000 genomes]
rs6656255	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696381	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6790	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs941987	0.83[EUR][1000 genomes]
rs941988	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9970048	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 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	chr1:173794400-173832800	Weak transcription	Fetal Heart	heart
2	chr1:173794600-173832000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:173794600-173832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:173794600-173832600	Weak transcription	Brain Substantia Nigra	brain
5	chr1:173794600-173833800	Weak transcription	Stomach Mucosa	stomach
6	chr1:173794800-173834000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:173795000-173834600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:173809800-173831800	Weak transcription	Colonic Mucosa	Colon
9	chr1:173813200-173831800	Weak transcription	Right Ventricle	heart
10	chr1:173813200-173832000	Weak transcription	Small Intestine	intestine
11	chr1:173818200-173831600	Weak transcription	Fetal Brain Male	brain
12	chr1:173818600-173834800	Strong transcription	Fetal Muscle Leg	muscle
13	chr1:173818600-173834800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr1:173819200-173833200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:173819200-173833800	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:173819200-173834000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:173819400-173832000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:173819400-173834800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:173819600-173834000	Strong transcription	Fetal Thymus	thymus
20	chr1:173819600-173835600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr1:173820600-173833800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:173820600-173834000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr1:173821000-173834000	Strong transcription	Liver	Liver
24	chr1:173821000-173834000	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr1:173822000-173834000	Strong transcription	Fetal Intestine Large	intestine
26	chr1:173822400-173832600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:173822400-173833600	Strong transcription	Fetal Brain Female	brain
28	chr1:173822400-173833800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:173822800-173831800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:173822800-173832400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:173822800-173832400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr1:173822800-173833400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:173822800-173834800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:173823000-173831600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:173823000-173831800	Weak transcription	NHLF	lung
36	chr1:173823000-173835000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:173823200-173833400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:173823400-173831400	Weak transcription	Pancreas	Pancrea
39	chr1:173823400-173832200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:173824600-173833800	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:173824800-173834600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr1:173825200-173832200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:173825600-173832000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr1:173825600-173832400	Weak transcription	Brain Angular Gyrus	brain
45	chr1:173826400-173831400	Weak transcription	Gastric	stomach
46	chr1:173826800-173832200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:173827000-173831600	Weak transcription	Esophagus	oesophagus
48	chr1:173827000-173831800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:173827000-173832000	Weak transcription	HUVEC	blood vessel
50	chr1:173827000-173832000	Weak transcription	NHEK	skin

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