Variant report

Variant	rs12409108
Chromosome Location	chr1:176139563-176139564
allele	A/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: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10494498	0.85[EUR][1000 genomes]
rs10798446	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10798447	0.81[EUR][1000 genomes]
rs10913133	0.81[EUR][1000 genomes]
rs10913134	0.81[EUR][1000 genomes]
rs10913135	0.81[EUR][1000 genomes]
rs10913142	0.84[EUR][1000 genomes]
rs10913143	0.83[EUR][1000 genomes]
rs10913144	0.84[EUR][1000 genomes]
rs10913145	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10913147	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10913148	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12033997	0.84[EUR][1000 genomes]
rs12034255	0.84[EUR][1000 genomes]
rs12039741	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12042918	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12047295	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12049077	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12724558	0.85[ASN][1000 genomes]
rs12755507	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17354120	0.82[EUR][1000 genomes]
rs2861672	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34215167	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34511428	0.83[EUR][1000 genomes]
rs3748618	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4526571	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6673760	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6678628	0.80[EUR][1000 genomes]
rs6678812	0.80[EUR][1000 genomes]
rs6684140	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7514517	0.83[EUR][1000 genomes]
rs7517503	0.82[EUR][1000 genomes]
rs7522843	0.80[EUR][1000 genomes]
rs7553759	0.82[EUR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12409108	RP11-318C24.2	cis	Whole Blood	GTEx

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	chr1:176127400-176139600	Weak transcription	Brain Anterior Caudate	brain
19	chr1:176127400-176140200	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:176127400-176141200	Weak transcription	HMEC	breast
21	chr1:176127400-176143200	Weak transcription	Brain Substantia Nigra	brain
22	chr1:176127400-176144200	Weak transcription	A549	lung
23	chr1:176127400-176153400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:176127400-176155400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:176128000-176139600	Weak transcription	Psoas Muscle	Psoas
26	chr1:176128000-176144200	Weak transcription	Gastric	stomach
27	chr1:176128000-176147000	Weak transcription	Stomach Mucosa	stomach
28	chr1:176128000-176157800	Weak transcription	Spleen	Spleen
29	chr1:176128000-176175200	Weak transcription	Esophagus	oesophagus
30	chr1:176128200-176139600	Weak transcription	Fetal Intestine Small	intestine
31	chr1:176128400-176154600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:176128600-176147000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:176128600-176147200	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr1:176128600-176155600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:176128800-176152800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr1:176128800-176152800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:176128800-176154200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:176130200-176140400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:176130200-176140600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:176130400-176141800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:176130400-176143200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:176130800-176140600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:176130800-176141000	Weak transcription	Ovary	ovary
44	chr1:176130800-176141600	Weak transcription	Fetal Heart	heart
45	chr1:176131000-176139800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:176131000-176139800	Weak transcription	Thymus	Thymus
47	chr1:176131000-176143400	Weak transcription	NHDF-Ad	bronchial
48	chr1:176131000-176144000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:176131200-176141800	Weak transcription	HepG2	liver
50	chr1:176131400-176140400	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links