Variant report

Variant	rs2481660
Chromosome Location	chr1:176139656-176139657
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:176139119..176142139-chr6:26032575..26034849,4	MCF-7	breast:
2	chr1:176139139..176142119-chr6:26031592..26033955,2	K562	blood:

Variant related genes	Relation type
ENSG00000124693	Chromatin interaction
ENSG00000137259	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10158829	0.91[ASN][1000 genomes]
rs10737316	1.00[AMR][1000 genomes]
rs10798431	0.95[AMR][1000 genomes]
rs10798433	1.00[AMR][1000 genomes]
rs10798435	1.00[AMR][1000 genomes]
rs11804926	0.91[ASN][1000 genomes]
rs11809136	0.91[ASN][1000 genomes]
rs11809835	0.91[ASN][1000 genomes]
rs12239888	0.91[ASN][1000 genomes]
rs16849571	0.91[ASN][1000 genomes]
rs1831447	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2039232	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2481639	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2481653	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2502824	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2502825	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3845368	0.91[ASN][1000 genomes]
rs4304533	1.00[AMR][1000 genomes]
rs4543747	1.00[AMR][1000 genomes]
rs4650936	0.91[ASN][1000 genomes]
rs4652150	0.85[ASN][1000 genomes]
rs4652151	0.91[ASN][1000 genomes]
rs4652152	0.91[ASN][1000 genomes]
rs4652154	0.88[ASN][1000 genomes]
rs4652155	0.88[ASN][1000 genomes]
rs559341	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs55969691	0.91[ASN][1000 genomes]
rs56981673	0.91[ASN][1000 genomes]
rs57395528	0.91[ASN][1000 genomes]
rs58178699	0.91[ASN][1000 genomes]
rs58305404	0.88[ASN][1000 genomes]
rs58325269	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58743849	0.91[ASN][1000 genomes]
rs59373738	0.91[ASN][1000 genomes]
rs598177	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs599326	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs602933	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61451700	0.91[ASN][1000 genomes]
rs6425370	1.00[AMR][1000 genomes]
rs6672278	0.90[AMR][1000 genomes]
rs704825	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs704830	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs704831	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73040940	0.91[ASN][1000 genomes]
rs73040951	0.91[ASN][1000 genomes]
rs73042718	0.91[ASN][1000 genomes]
rs73042723	0.91[ASN][1000 genomes]
rs73042728	0.80[ASN][1000 genomes]
rs73042741	0.91[ASN][1000 genomes]
rs73042749	0.91[ASN][1000 genomes]
rs74127190	0.91[ASN][1000 genomes]
rs7521561	0.91[ASN][1000 genomes]
rs7536464	0.90[AMR][1000 genomes]
rs7543769	0.95[AMR][1000 genomes]
rs796933	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs796934	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv872565	chr1:176058782-176172795	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv8558	chr1:176135063-176141916	Enhancers Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176055000-176141600	Weak transcription	Hela-S3	cervix
2	chr1:176065600-176154800	Weak transcription	Aorta	Aorta
3	chr1:176070400-176151400	Weak transcription	Pancreas	Pancrea
4	chr1:176072000-176140600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:176085400-176142400	Weak transcription	Lung	lung
6	chr1:176100800-176153200	Weak transcription	Colonic Mucosa	Colon
7	chr1:176110600-176164000	Weak transcription	NHLF	lung
8	chr1:176116000-176146200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:176122000-176139800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:176123800-176139800	Weak transcription	Fetal Kidney	kidney
11	chr1:176123800-176144200	Weak transcription	Left Ventricle	heart
12	chr1:176123800-176150000	Weak transcription	Osteobl	bone
13	chr1:176126400-176168800	Weak transcription	Small Intestine	intestine
14	chr1:176126800-176139800	Weak transcription	HSMMtube	muscle
15	chr1:176127000-176147000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:176127000-176174000	Weak transcription	Colon Smooth Muscle	Colon
17	chr1:176127200-176153400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:176127400-176140200	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:176127400-176141200	Weak transcription	HMEC	breast
20	chr1:176127400-176143200	Weak transcription	Brain Substantia Nigra	brain
21	chr1:176127400-176144200	Weak transcription	A549	lung
22	chr1:176127400-176153400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:176127400-176155400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:176128000-176144200	Weak transcription	Gastric	stomach
25	chr1:176128000-176147000	Weak transcription	Stomach Mucosa	stomach
26	chr1:176128000-176157800	Weak transcription	Spleen	Spleen
27	chr1:176128000-176175200	Weak transcription	Esophagus	oesophagus
28	chr1:176128400-176154600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:176128600-176147000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr1:176128600-176147200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr1:176128600-176155600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:176128800-176152800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:176128800-176152800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:176128800-176154200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:176130200-176140400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:176130200-176140600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:176130400-176141800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:176130400-176143200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:176130800-176140600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr1:176130800-176141000	Weak transcription	Ovary	ovary
41	chr1:176130800-176141600	Weak transcription	Fetal Heart	heart
42	chr1:176131000-176139800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:176131000-176139800	Weak transcription	Thymus	Thymus
44	chr1:176131000-176143400	Weak transcription	NHDF-Ad	bronchial
45	chr1:176131000-176144000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:176131200-176141800	Weak transcription	HepG2	liver
47	chr1:176131400-176140400	Weak transcription	K562	blood
48	chr1:176131400-176142600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:176131600-176139800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:176131800-176143600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links