Variant report

Variant	rs1638456
Chromosome Location	chr11:16879837-16879838
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:16878376..16881248-chr11:16883308..16886375,3	MCF-7	breast:
2	chr11:16874547..16876364-chr11:16879183..16881324,2	MCF-7	breast:
3	chr11:16878202..16880013-chr11:16893288..16895132,2	K562	blood:
4	chr11:16869293..16871561-chr11:16878858..16881277,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs12418111	0.84[ASN][1000 genomes]
rs1638457	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16933675	0.84[ASN][1000 genomes]
rs177546	0.81[ASN][1000 genomes]
rs177554	0.81[ASN][1000 genomes]
rs370053	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs370671	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs373266	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs376641	0.80[EUR][1000 genomes]
rs378863	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs380655	0.80[AMR][1000 genomes]
rs381815	0.90[ASN][1000 genomes]
rs382280	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs385627	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs385943	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs387849	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs388968	0.86[ASN][1000 genomes]
rs389967	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs391332	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs392706	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs393633	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs397343	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs397373	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs398216	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs400085	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs400349	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs406109	0.85[AMR][1000 genomes]
rs406890	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs406937	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs407354	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs407932	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs409354	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs413858	0.88[ASN][1000 genomes]
rs414219	0.93[ASN][1000 genomes]
rs414992	0.94[ASN][1000 genomes]
rs415265	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs417406	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs420975	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs422272	0.88[ASN][1000 genomes]
rs425325	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs426085	0.85[AMR][1000 genomes]
rs427429	0.90[ASN][1000 genomes]
rs428840	0.91[ASN][1000 genomes]
rs429368	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs430211	0.82[AMR][1000 genomes]
rs432046	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs434899	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs435206	0.93[ASN][1000 genomes]
rs443327	0.83[AMR][1000 genomes]
rs445146	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs445205	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs445431	0.93[ASN][1000 genomes]
rs446518	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs446612	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs448671	0.90[ASN][1000 genomes]
rs450828	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs452414	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs453015	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs454538	0.85[AMR][1000 genomes]
rs58542530	0.86[ASN][1000 genomes]
rs61882035	0.86[ASN][1000 genomes]
rs61882036	0.86[ASN][1000 genomes]
rs61882037	0.86[ASN][1000 genomes]
rs61882038	0.84[ASN][1000 genomes]
rs758402	0.81[ASN][1000 genomes]
rs7926335	0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832077	chr11:16834545-17059176	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16853400-16883800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr11:16861800-16880600	Weak transcription	HMEC	breast
3	chr11:16863400-16882000	Weak transcription	Stomach Mucosa	stomach
4	chr11:16863800-16884800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr11:16863800-16892600	Weak transcription	Fetal Kidney	kidney
6	chr11:16864200-16882000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr11:16867800-16885000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:16872000-16895800	Weak transcription	Aorta	Aorta
9	chr11:16872200-16882200	Weak transcription	Brain Angular Gyrus	brain
10	chr11:16872200-16884400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:16872600-16889600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr11:16872800-16883800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr11:16873000-16881200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr11:16874400-16881400	Strong transcription	Fetal Intestine Small	intestine
15	chr11:16876000-16881200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:16876000-16883800	Weak transcription	Fetal Brain Female	brain
17	chr11:16876200-16888400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:16876400-16880000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr11:16876400-16883600	Weak transcription	Spleen	Spleen
20	chr11:16876600-16884000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:16876600-16889800	Weak transcription	Adipose Nuclei	Adipose
22	chr11:16876600-16890800	Weak transcription	Colonic Mucosa	Colon
23	chr11:16876800-16881600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:16876800-16898600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr11:16877600-16880400	Weak transcription	Placenta	Placenta
26	chr11:16877800-16883800	Weak transcription	Brain Germinal Matrix	brain
27	chr11:16877800-16890000	Weak transcription	Lung	lung
28	chr11:16877800-16892200	Weak transcription	Fetal Stomach	stomach
29	chr11:16877800-16899600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr11:16878000-16889400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr11:16878200-16881600	Weak transcription	Brain Hippocampus Middle	brain
32	chr11:16878200-16883800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:16878400-16881400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr11:16878400-16883400	Weak transcription	Brain Substantia Nigra	brain
35	chr11:16878600-16880400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr11:16878600-16880400	Weak transcription	Right Atrium	heart
37	chr11:16878600-16882200	Weak transcription	Brain Anterior Caudate	brain
38	chr11:16878800-16881200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr11:16878800-16890000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr11:16879000-16880400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:16879000-16880400	Weak transcription	Left Ventricle	heart
42	chr11:16879000-16880600	Weak transcription	HepG2	liver
43	chr11:16879000-16881000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:16879000-16881200	Weak transcription	Pancreas	Pancrea
45	chr11:16879000-16881400	Weak transcription	Gastric	stomach
46	chr11:16879000-16881800	Weak transcription	Psoas Muscle	Psoas
47	chr11:16879000-16883600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr11:16879000-16884200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr11:16879000-16887600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr11:16879200-16880400	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links