Variant report

Variant	rs1572229
Chromosome Location	chr6:150064977-150064978
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150063981..150065532-chr6:150069623..150071188,2	K562	blood:
2	chr6:150061815..150065495-chr6:150065702..150069164,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120253	Chromatin interaction
ENSG00000120265	Chromatin interaction

Extended variants
information (count: 144 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs10214845	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs10457851	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs10747276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10782310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10782312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10782316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs10782317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs10782318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10872646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs10872647	0.96[CEU][hapmap]
rs10872650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs10872656	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs1108889	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs1112730	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap]
rs11155662	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11155670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11155671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11155674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11155685	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs11155689	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs1125	0.96[CEU][hapmap]
rs12174349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12176034	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12195866	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs12210605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12234128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12526675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12528279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs12529698	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12660304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1413654	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs1413655	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs1934534	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2064520	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2064521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2065663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2065664	0.95[CEU][hapmap];0.80[CHB][hapmap];0.88[JPT][hapmap]
rs2095375	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs2151913	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs2185352	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2275045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2275046	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs2297930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2342764	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2342765	0.95[CEU][hapmap]
rs2342858	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs2880436	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs35031906	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs3734295	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3763162	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs3763163	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs3777949	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3798761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3805749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3805753	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs3924871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4242279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4354168	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4421206	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4455682	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4552	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs4816	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs4869731	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs4869750	0.95[CEU][hapmap]
rs4870050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4870052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4870054	0.95[CEU][hapmap]
rs4870509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4870529	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6903998	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs6913486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7450246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7738696	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs7740278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7744105	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs7752089	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7753812	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs7767622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7769115	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs7818	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs868375	0.96[CEU][hapmap]
rs880245	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs880246	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs9027	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs9285521	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs9285524	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs9322188	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9322189	0.88[CEU][hapmap]
rs9322193	0.91[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs9322198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9322200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9322206	0.95[CEU][hapmap];0.80[CHB][hapmap];0.88[JPT][hapmap]
rs9322209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9322214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9322218	0.95[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap]
rs9322219	0.91[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs933055	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs9371201	0.95[CEU][hapmap]
rs9372044	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs9377229	0.91[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs9377230	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9383546	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs9393175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9397357	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs9404048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9478291	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap]
rs9478848	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs9479094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9479808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap]
rs9479810	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap]
rs9505974	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs952165	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs958953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9688350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9688412	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs9688452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9688699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9689036	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap]
rs9689084	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9689269	0.91[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap]
rs9689702	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs9689723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9718079	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9766004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9766037	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9766562	0.92[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs9766886	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9767105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9767122	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs9767123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9767309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9767555	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9767713	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9800580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9800614	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9800686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9800736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9800806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs9968911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886762	chr6:149866452-150174507	Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1792620	chr6:149909491-150083621	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	esv3475167	chr6:150003006-150086225	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv3475168	chr6:150003006-150086225	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	esv1803291	chr6:150018508-150164190	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1572229	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs1572229	C6orf72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150039800-150066800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:150039800-150067000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:150040000-150066600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:150040400-150066200	Weak transcription	Fetal Brain Male	brain
5	chr6:150043600-150065600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:150043600-150066000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:150044000-150065200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:150044000-150065400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:150044200-150065000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:150044200-150065200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:150044800-150065000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:150045400-150065600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:150045800-150065400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:150046600-150065000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr6:150048400-150066600	Weak transcription	Fetal Heart	heart
16	chr6:150049000-150065600	Strong transcription	Fetal Stomach	stomach
17	chr6:150049800-150065200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:150050000-150065200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr6:150050000-150065600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:150050200-150065200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr6:150050200-150066600	Weak transcription	Stomach Mucosa	stomach
22	chr6:150050400-150066400	Strong transcription	Fetal Intestine Small	intestine
23	chr6:150050600-150065400	Strong transcription	Fetal Thymus	thymus
24	chr6:150051000-150065000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:150051000-150065200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr6:150051000-150065600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:150051200-150065200	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr6:150052200-150065400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr6:150052200-150066800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:150052400-150065400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:150053800-150065400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:150054400-150065200	Strong transcription	K562	blood
33	chr6:150054400-150065400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:150054600-150065200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr6:150054600-150065200	Strong transcription	Dnd41	blood
36	chr6:150055000-150065200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:150058800-150066600	Weak transcription	HSMMtube	muscle
38	chr6:150059600-150065000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr6:150059600-150065200	Strong transcription	Primary B cells from cord blood	blood
40	chr6:150059800-150065200	Strong transcription	Primary T cells from cord blood	blood
41	chr6:150060000-150065200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr6:150060000-150065400	Strong transcription	Fetal Muscle Leg	muscle
43	chr6:150060200-150065400	Strong transcription	Fetal Muscle Trunk	muscle
44	chr6:150060400-150065200	Strong transcription	Brain Hippocampus Middle	brain
45	chr6:150060400-150065200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr6:150060400-150065200	Strong transcription	Fetal Intestine Large	intestine
47	chr6:150060800-150065000	Strong transcription	Fetal Lung	lung
48	chr6:150060800-150065000	Strong transcription	Osteobl	bone
49	chr6:150060800-150065200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr6:150061200-150066800	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links