Variant report

Variant	rs11892744
Chromosome Location	chr2:99237792-99237793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99236596..99238739-chr2:99240851..99242868,2	MCF-7	breast:
2	chr2:99223676..99231123-chr2:99236273..99243561,12	MCF-7	breast:
3	chr2:99233497..99236198-chr2:99236599..99238658,2	MCF-7	breast:
4	chr2:64880921..64881475-chr2:99237561..99238097,2	NB4	blood:
5	chr2:99223477..99227103-chr2:99237470..99240691,6	MCF-7	breast:
6	chr2:99232801..99235127-chr2:99235429..99239328,4	MCF-7	breast:
7	chr2:99236937..99238567-chr2:99240106..99242070,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179833	Chromatin interaction
ENSG00000183513	Chromatin interaction
ENSG00000115446	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10496327	0.93[CHB][hapmap]
rs1139829	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11537554	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11884553	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs11896729	0.85[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12618524	0.92[CHB][hapmap]
rs13402379	0.85[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1516085	0.85[CEU][hapmap];0.94[CHD][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1587835	0.94[CHB][hapmap]
rs17031905	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs17032866	0.81[CHB][hapmap]
rs17032870	0.81[CHB][hapmap]
rs17033813	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17034171	0.85[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17034241	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17444095	0.94[CHB][hapmap];0.94[CHD][hapmap];0.85[TSI][hapmap]
rs17446058	0.94[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17504774	0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs17505326	0.94[CHB][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17506535	0.85[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17513468	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2230388	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2276603	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2278206	0.81[EUR][1000 genomes]
rs2278207	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2278208	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2278212	0.81[CHB][hapmap]
rs2278213	0.81[CHB][hapmap];0.91[CHD][hapmap];0.84[TSI][hapmap]
rs2278214	0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs3203856	0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34906456	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3729568	0.81[CHB][hapmap];0.91[CHD][hapmap];0.82[TSI][hapmap]
rs3754871	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3754872	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3754875	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3754877	0.81[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3754878	0.81[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3754879	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3754880	0.81[CHB][hapmap]
rs3754881	0.81[CHB][hapmap];0.91[CHD][hapmap];0.82[TSI][hapmap]
rs3754891	0.81[CHB][hapmap]
rs3754892	0.92[CHB][hapmap]
rs3769698	0.85[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3769701	0.81[CHB][hapmap];0.86[EUR][1000 genomes]
rs3769708	0.81[CEU][hapmap];0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs3769709	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3769712	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3769713	0.82[EUR][1000 genomes]
rs3769715	0.94[CHB][hapmap]
rs3769716	0.94[CHB][hapmap]
rs3769719	0.81[CHB][hapmap]
rs3769727	0.81[CHB][hapmap]
rs3769728	0.94[CHB][hapmap]
rs3769729	0.81[CHB][hapmap]
rs3769734	0.94[CHB][hapmap]
rs3769735	0.82[EUR][1000 genomes]
rs3769737	0.94[CHB][hapmap];0.91[CHD][hapmap];0.84[TSI][hapmap]
rs3769740	0.81[CHB][hapmap];0.89[CHD][hapmap];0.82[TSI][hapmap]
rs3769741	0.81[CHB][hapmap];0.91[CHD][hapmap];0.82[TSI][hapmap]
rs3769743	0.81[CHB][hapmap]
rs3820941	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3820943	0.94[CHB][hapmap]
rs4850874	0.81[CHB][hapmap]
rs4850875	0.94[CHB][hapmap]
rs4851136	0.94[CHB][hapmap]
rs4851138	0.81[CHB][hapmap]
rs4851142	0.81[CHB][hapmap]
rs4851144	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4851145	0.85[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851146	0.85[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6736755	0.85[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs72821951	0.82[EUR][1000 genomes]
rs72821955	0.81[EUR][1000 genomes]
rs72821956	0.81[EUR][1000 genomes]
rs72821965	0.85[EUR][1000 genomes]
rs72823788	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72823792	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72823794	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72823796	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72823801	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7562232	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7585747	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7585939	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7588254	0.85[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7595120	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013941	chr2:99116255-99317933	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv535834	chr2:99116255-99317933	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11892744	UNC50	cis	lymphoblastoid	seeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99226800-99238600	Strong transcription	Primary B cells from cord blood	blood
2	chr2:99227000-99239000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:99227200-99257400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr2:99227600-99243200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr2:99227800-99239400	Strong transcription	HUVEC	blood vessel
6	chr2:99227800-99240200	Strong transcription	Fetal Thymus	thymus
7	chr2:99228000-99238200	Strong transcription	Adipose Nuclei	Adipose
8	chr2:99228000-99239000	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:99228000-99240000	Strong transcription	Dnd41	blood
10	chr2:99228000-99240400	Strong transcription	Duodenum Mucosa	Duodenum
11	chr2:99228000-99241200	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr2:99228200-99240400	Strong transcription	Fetal Intestine Large	intestine
13	chr2:99228200-99244600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:99229000-99240800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:99229400-99238600	Strong transcription	Brain Cingulate Gyrus	brain
16	chr2:99229400-99242400	Strong transcription	HepG2	liver
17	chr2:99230200-99250600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:99231200-99247600	Weak transcription	Brain Angular Gyrus	brain
19	chr2:99231200-99286200	Weak transcription	Stomach Mucosa	stomach
20	chr2:99232400-99238400	Weak transcription	Gastric	stomach
21	chr2:99232400-99239000	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr2:99232400-99239200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:99232400-99249000	Weak transcription	Psoas Muscle	Psoas
24	chr2:99232400-99250600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:99232600-99249400	Weak transcription	Aorta	Aorta
26	chr2:99232800-99239000	Weak transcription	Fetal Brain Male	brain
27	chr2:99232800-99250000	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:99233400-99247200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:99233800-99247600	Weak transcription	Spleen	Spleen
30	chr2:99234000-99238200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:99234000-99239200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:99234000-99252800	Weak transcription	Brain Germinal Matrix	brain
33	chr2:99234200-99237800	Weak transcription	Brain Anterior Caudate	brain
34	chr2:99234200-99247600	Weak transcription	Fetal Stomach	stomach
35	chr2:99234400-99247400	Weak transcription	Right Ventricle	heart
36	chr2:99234400-99251000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:99234600-99237800	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:99234600-99239000	Weak transcription	Lung	lung
39	chr2:99234600-99310600	Weak transcription	Small Intestine	intestine
40	chr2:99234800-99238000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:99234800-99240200	Weak transcription	GM12878-XiMat	blood
42	chr2:99234800-99242400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:99234800-99248400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:99234800-99250800	Weak transcription	Fetal Muscle Leg	muscle
45	chr2:99234800-99264600	Weak transcription	Ovary	ovary
46	chr2:99234800-99296400	Weak transcription	Esophagus	oesophagus
47	chr2:99235000-99240600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:99235000-99247200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr2:99235200-99238400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:99235200-99239000	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links