Variant report

Variant	rs16933675
Chromosome Location	chr11:16919677-16919678
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:16918607..16920232-chr8:87576439..87578551,2	MCF-7	breast:
2	chr11:16912383..16915657-chr11:16918244..16920114,3	K562	blood:
3	chr11:16912383..16915251-chr11:16918244..16921230,3	K562	blood:

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10741713	0.88[JPT][hapmap]
rs10766360	0.88[CHD][hapmap];0.88[JPT][hapmap]
rs11024074	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs11024087	0.86[JPT][hapmap]
rs12418111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1638456	0.84[ASN][1000 genomes]
rs1638457	0.86[ASN][1000 genomes]
rs16933680	0.92[CEU][hapmap];0.86[CHB][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.81[ASN][1000 genomes]
rs16933682	0.92[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs16933683	0.88[JPT][hapmap]
rs16933684	0.88[CHD][hapmap];0.88[JPT][hapmap]
rs177544	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs177546	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs177551	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs177554	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs177561	0.88[JPT][hapmap]
rs177562	0.88[JPT][hapmap]
rs177563	0.87[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap]
rs2057788	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs2190752	0.88[JPT][hapmap]
rs2883150	0.88[JPT][hapmap]
rs35005405	0.81[ASN][1000 genomes]
rs35109048	0.83[ASN][1000 genomes]
rs369457	0.88[CHB][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs371905	0.88[CHB][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs378863	0.86[ASN][1000 genomes]
rs381815	0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs382280	0.88[CHB][hapmap]
rs387849	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs388968	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs389967	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs390974	0.88[CHB][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs391332	0.83[ASN][1000 genomes]
rs393633	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs397343	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs397373	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs400085	0.88[CHB][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs400349	0.88[CHB][hapmap]
rs400458	0.88[JPT][hapmap]
rs401820	0.88[CHB][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs402982	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs406890	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs407354	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs407932	0.88[CHB][hapmap]
rs409354	1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[TSI][hapmap]
rs413858	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs414219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs414992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs416258	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs417406	0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs420975	0.88[CHB][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap]
rs422272	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs425325	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs425745	0.84[CHB][hapmap]
rs427429	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs428840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs428933	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs430211	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs431208	0.88[JPT][hapmap]
rs432046	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs433212	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs433225	0.88[CHB][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs434761	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs434899	1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs435206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs440212	0.88[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs445146	0.88[CHB][hapmap];0.87[JPT][hapmap]
rs445205	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs445431	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs446518	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs448671	0.88[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs450828	0.88[CHB][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs452414	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs452745	0.88[CHB][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs454869	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs4756875	0.88[CHD][hapmap];0.88[JPT][hapmap]
rs4756876	0.88[CHD][hapmap];0.88[JPT][hapmap]
rs4757445	0.83[ASN][1000 genomes]
rs4757449	0.88[CHD][hapmap];0.88[JPT][hapmap]
rs4757451	0.88[JPT][hapmap]
rs4757452	0.87[JPT][hapmap]
rs4757454	0.88[CHD][hapmap];0.88[JPT][hapmap]
rs4757456	0.88[CHD][hapmap];0.88[JPT][hapmap]
rs4757457	0.88[CHD][hapmap];0.88[JPT][hapmap]
rs58542530	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59828007	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882035	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61882036	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61882037	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61882038	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486326	0.88[JPT][hapmap]
rs7111470	0.88[JPT][hapmap]
rs7396552	0.83[JPT][hapmap]
rs7481080	0.83[JPT][hapmap]
rs758402	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7924696	0.88[JPT][hapmap]
rs7926335	0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7926392	0.90[YRI][hapmap]
rs7931046	0.80[YRI][hapmap]
rs7939987	0.88[JPT][hapmap]
rs7947282	1.00[YRI][hapmap]
rs7947562	0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
2	nsv7688	chr11:16912759-16939804	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv2757425	chr11:16915291-16934130	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv2759805	chr11:16915291-16934130	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1038987	chr11:16916438-16927022	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv2754709	chr11:16917219-16927022	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16933675	SAA1	cis	parietal	SCAN
rs16933675	PIK3C2A	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16912200-16923600	Weak transcription	A549	lung
2	chr11:16913800-16921800	Enhancers	Fetal Heart	heart
3	chr11:16914000-16927400	Weak transcription	HSMMtube	muscle
4	chr11:16914600-16921200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr11:16915800-16921400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:16915800-16921400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:16915800-16922800	Weak transcription	HMEC	breast
8	chr11:16916000-16923000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:16916000-16924400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr11:16916000-16931000	Weak transcription	Spleen	Spleen
11	chr11:16916800-16920200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr11:16917600-16920200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:16917800-16922000	Enhancers	Stomach Mucosa	stomach
14	chr11:16918200-16919800	Enhancers	Fetal Lung	lung
15	chr11:16918200-16922400	Enhancers	Fetal Intestine Large	intestine
16	chr11:16918200-16924800	Weak transcription	Colonic Mucosa	Colon
17	chr11:16918400-16919800	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr11:16918400-16919800	Enhancers	Small Intestine	intestine
19	chr11:16918400-16920600	Enhancers	H9 Cell Line	embryonic stem cell
20	chr11:16918600-16920400	Enhancers	Brain Anterior Caudate	brain
21	chr11:16918600-16922000	Enhancers	Duodenum Mucosa	Duodenum
22	chr11:16918800-16919800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr11:16918800-16920000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:16918800-16920200	Enhancers	Adipose Nuclei	Adipose
25	chr11:16918800-16920200	Enhancers	Brain Hippocampus Middle	brain
26	chr11:16919000-16919800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
27	chr11:16919000-16919800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
28	chr11:16919000-16919800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
29	chr11:16919000-16919800	Enhancers	Primary hematopoietic stem cells	blood
30	chr11:16919000-16919800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:16919000-16919800	Enhancers	Left Ventricle	heart
32	chr11:16919000-16920000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:16919000-16920000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr11:16919000-16920400	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr11:16919000-16920400	Enhancers	HUVEC	blood vessel
36	chr11:16919200-16919800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr11:16919200-16919800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr11:16919200-16921400	Weak transcription	Pancreas	Pancrea
39	chr11:16919400-16919800	Enhancers	Fetal Kidney	kidney
40	chr11:16919400-16920200	Enhancers	Brain Angular Gyrus	brain
41	chr11:16919400-16921400	Weak transcription	Gastric	stomach
42	chr11:16919400-16922400	Enhancers	Fetal Intestine Small	intestine
43	chr11:16919400-16927000	Weak transcription	Fetal Muscle Leg	muscle
44	chr11:16919600-16920000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
45	chr11:16919600-16920000	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr11:16919600-16920000	Weak transcription	Liver	Liver
47	chr11:16919600-16920200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr11:16919600-16920200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:16919600-16920200	Weak transcription	Right Atrium	heart
50	chr11:16919600-16920400	Enhancers	H1 Cell Line	embryonic stem cell

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