Variant report

Variant	rs1001421
Chromosome Location	chr6:161567968-161567969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:161548242..161551323-chr6:161565381..161568765,4	K562	blood:
2	chr6:161566087..161569641-chr6:161785856..161789665,3	K562	blood:
3	chr6:161561291..161565490-chr6:161565996..161568943,5	K562	blood:
4	chr6:161564867..161570084-chr6:161571350..161575451,5	K562	blood:
5	chr6:161551128..161553657-chr6:161566830..161569140,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1001422	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs1001756	1.00[CHB][hapmap]
rs11751634	1.00[CHB][hapmap]
rs11751843	1.00[CHB][hapmap]
rs11752188	1.00[CHB][hapmap]
rs11757223	1.00[CHB][hapmap]
rs11757309	1.00[CHB][hapmap]
rs11757882	1.00[CHB][hapmap]
rs11758794	1.00[CHB][hapmap]
rs11759408	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs11962121	1.00[CHB][hapmap]
rs12110827	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs1404269	1.00[CHB][hapmap]
rs1464781	1.00[CHB][hapmap]
rs1474914	0.86[EUR][1000 genomes]
rs1534020	1.00[CHB][hapmap]
rs1562025	1.00[CHB][hapmap]
rs1807426	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs1880367	0.81[CEU][hapmap];0.85[ASN][1000 genomes]
rs2009830	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2314190	0.93[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2314376	1.00[CHB][hapmap]
rs2314377	1.00[CHB][hapmap]
rs3778218	1.00[CHB][hapmap]
rs3778221	0.83[ASN][1000 genomes]
rs3778225	1.00[CHB][hapmap]
rs3798916	1.00[CHB][hapmap]
rs3823057	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs41268545	0.83[ASN][1000 genomes]
rs55799452	0.83[ASN][1000 genomes]
rs6455707	0.86[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6905734	1.00[CHB][hapmap]
rs6940321	1.00[CHB][hapmap]
rs7752907	0.85[ASN][1000 genomes]
rs7754215	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs7754525	0.95[ASN][1000 genomes]
rs9365245	1.00[CHB][hapmap]
rs9456635	1.00[CHB][hapmap]
rs9458121	1.00[CHB][hapmap]
rs9458135	1.00[CHB][hapmap]
rs9458141	1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

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	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1030852	chr6:161477750-161589394	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv3513382	chr6:161564862-161568560	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv3513383	chr6:161565312-161568410	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3513384	chr6:161565312-161568410	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1001421	AGPAT4	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161541000-161584600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:161542000-161585600	Weak transcription	Fetal Kidney	kidney
3	chr6:161544600-161589600	Weak transcription	Fetal Brain Male	brain
4	chr6:161545000-161584800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:161548400-161590800	Weak transcription	Fetal Thymus	thymus
6	chr6:161549200-161577000	Strong transcription	Fetal Brain Female	brain
7	chr6:161549200-161577400	Strong transcription	Fetal Stomach	stomach
8	chr6:161549800-161589400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:161550000-161584600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:161550200-161577400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:161553200-161569600	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:161553400-161571800	Weak transcription	HUVEC	blood vessel
13	chr6:161553800-161586600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr6:161554000-161574000	Weak transcription	Pancreas	Pancrea
15	chr6:161554000-161591000	Weak transcription	Colonic Mucosa	Colon
16	chr6:161555000-161585000	Weak transcription	Right Atrium	heart
17	chr6:161555600-161568800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:161555800-161586600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:161557600-161569200	Weak transcription	Aorta	Aorta
20	chr6:161557600-161574400	Weak transcription	Gastric	stomach
21	chr6:161557600-161581400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:161557800-161584200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr6:161558200-161571400	Weak transcription	Thymus	Thymus
24	chr6:161558200-161571800	Weak transcription	Primary B cells from cord blood	blood
25	chr6:161558200-161577800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:161558200-161582600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:161558200-161589400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:161558400-161581400	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:161558600-161574400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr6:161559400-161568200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:161559400-161587600	Weak transcription	Fetal Intestine Large	intestine
32	chr6:161560000-161583200	Weak transcription	HMEC	breast
33	chr6:161560200-161574800	Weak transcription	Right Ventricle	heart
34	chr6:161560200-161583800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:161560400-161568800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:161560400-161568800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:161560400-161571800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr6:161560400-161581400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr6:161560400-161584600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:161560600-161584400	Weak transcription	NHLF	lung
41	chr6:161560800-161568400	Weak transcription	HSMM	muscle
42	chr6:161560800-161582400	Weak transcription	HSMMtube	muscle
43	chr6:161561200-161574200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:161561600-161573600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:161561600-161573800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr6:161562000-161573600	Weak transcription	Fetal Intestine Small	intestine
47	chr6:161562400-161570600	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr6:161562600-161569200	Weak transcription	NHDF-Ad	bronchial
49	chr6:161562600-161570200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:161562600-161572800	Weak transcription	Fetal Heart	heart

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