Variant report

Variant	rs11165441
Chromosome Location	chr1:92224347-92224348
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	chr1:92221438..92225438-chr1:92226162..92228913,3	K562	blood:
2	chr1:92222836..92226137-chr1:92226478..92228913,3	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10493860	0.92[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10874925	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12121039	0.92[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12121065	0.92[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12127610	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12127644	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12128642	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12129174	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12133753	0.89[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17131550	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28406383	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7522702	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7526590	0.89[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7529421	0.89[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9887787	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9887957	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv949449	chr1:92211020-92585831	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv1826229	chr1:92215725-92233227	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv524845	chr1:92215725-92598705	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv462517	chr1:92215725-92598705	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv546810	chr1:92215725-92598705	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1006318	chr1:92216408-92608324	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv432498	chr1:92218245-92618323	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv1004570	chr1:92220544-92622129	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv1007661	chr1:92220544-92655952	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11165441	TMEM56	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92197600-92230000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:92198200-92224400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:92204800-92247000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:92208400-92235800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:92211800-92235600	Weak transcription	Fetal Kidney	kidney
6	chr1:92213800-92235000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:92215200-92232400	Weak transcription	A549	lung
8	chr1:92216800-92241800	Weak transcription	Aorta	Aorta
9	chr1:92217000-92226200	Weak transcription	Fetal Brain Male	brain
10	chr1:92217200-92230200	Weak transcription	Pancreas	Pancrea
11	chr1:92217400-92232400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:92217600-92230200	Weak transcription	Hela-S3	cervix
13	chr1:92217800-92225000	Weak transcription	Brain Angular Gyrus	brain
14	chr1:92217800-92247800	Weak transcription	Small Intestine	intestine
15	chr1:92218000-92224600	Weak transcription	Brain Anterior Caudate	brain
16	chr1:92218200-92225000	Strong transcription	HepG2	liver
17	chr1:92219000-92226600	Genic enhancers	NHDF-Ad	bronchial
18	chr1:92219400-92227600	Enhancers	Rectal Smooth Muscle	rectum
19	chr1:92219400-92238200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:92220200-92229000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:92220200-92229200	Weak transcription	Osteobl	bone
22	chr1:92220400-92230000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:92220400-92234000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:92220600-92226200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:92220600-92255800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:92221000-92224400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:92221000-92224600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr1:92221000-92248000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:92221800-92224800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:92221800-92225200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:92221800-92225400	Weak transcription	Psoas Muscle	Psoas
32	chr1:92222000-92226400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:92222200-92226400	Weak transcription	Fetal Heart	heart
34	chr1:92222200-92231000	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr1:92223000-92225000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:92223000-92227200	Enhancers	Liver	Liver
37	chr1:92223200-92224800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:92223200-92228000	Enhancers	Colon Smooth Muscle	Colon
39	chr1:92223400-92224400	Genic enhancers	Ovary	ovary
40	chr1:92223400-92229400	Enhancers	Adipose Nuclei	Adipose
41	chr1:92223600-92224400	Genic enhancers	Stomach Smooth Muscle	stomach
42	chr1:92223600-92224600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:92223600-92224600	Genic enhancers	Placenta	Placenta
44	chr1:92223600-92224600	Genic enhancers	NHLF	lung
45	chr1:92223800-92224400	Genic enhancers	Fetal Muscle Leg	muscle
46	chr1:92223800-92224800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:92223800-92224800	Enhancers	Right Ventricle	heart
48	chr1:92223800-92228400	Enhancers	Right Atrium	heart
49	chr1:92223800-92232000	Enhancers	K562	blood
50	chr1:92224000-92224400	Strong transcription	Fetal Muscle Trunk	muscle

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