Variant report

Variant	rs2999528
Chromosome Location	chr1:151952885-151952886
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151881739..151884643-chr1:151951894..151953889,2	K562	blood:
2	chr1:151951145..151953064-chr1:151955721..151958103,2	K562	blood:
3	chr1:151952034..151953973-chr1:152006565..152009947,3	MCF-7	breast:
4	chr1:151951212..151953064-chr1:151955112..151957221,2	K562	blood:

Variant related genes	Relation type
ENSG00000163191	Chromatin interaction
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1038747	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10494270	0.85[CHB][hapmap]
rs10788817	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs10788820	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11204915	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs11204922	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11542015	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11589720	0.87[ASN][1000 genomes]
rs12083193	0.91[CHB][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs12116923	0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs13320	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs1387833	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1532133	0.86[CHB][hapmap]
rs16833668	0.91[CHB][hapmap]
rs16833728	0.95[CHB][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap]
rs16833743	0.91[CHB][hapmap]
rs1979637	0.81[CHB][hapmap]
rs2279501	0.81[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2279502	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.88[ASN][1000 genomes]
rs2337689	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2338019	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2932570	0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2932574	0.82[ASN][1000 genomes]
rs2932579	0.91[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs2932581	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2932583	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2932586	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2932590	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999508	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2999512	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2999526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999531	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999534	0.83[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999539	0.83[ASW][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2999542	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs2999544	0.86[CHB][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs2999560	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2999561	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3007670	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs3007685	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs3007691	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3007708	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3007711	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs3791153	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs4845713	0.84[CHB][hapmap]
rs6587635	0.95[CHB][hapmap]
rs6587636	0.95[CHB][hapmap]
rs6587637	0.90[CHB][hapmap]
rs6587638	0.95[CHB][hapmap]
rs6587640	0.91[CHB][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.87[TSI][hapmap]
rs6662611	0.95[CHB][hapmap]
rs6663064	0.91[CHB][hapmap];0.81[TSI][hapmap]
rs6678672	0.91[CHB][hapmap];0.80[JPT][hapmap];0.85[TSI][hapmap]
rs6685187	0.85[MEX][hapmap];0.82[TSI][hapmap]
rs6686874	0.91[CHB][hapmap];0.81[TSI][hapmap]
rs6703465	0.95[CHB][hapmap]
rs7535002	0.91[CHB][hapmap]
rs7541099	0.95[CHB][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap]
rs902313	0.95[CHB][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap]
rs971887	0.95[CHB][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap]
rs9943221	0.86[CHB][hapmap];0.81[TSI][hapmap]
rs9943251	0.87[CHB][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	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer 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	191 gene(s)	inside rSNPs	diseases
6	nsv2855	chr1:151936470-151966381	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2999528	THEM4	cis	multi-tissue	Pritchard
rs2999528	SCNM1	cis	parietal	SCAN
rs2999528	S100A10	cis	cerebellum	SCAN
rs2999528	THEM4	cis	parietal	SCAN
rs2999528	S100A10	cis	multi-tissue	Pritchard
rs2999528	THEM4	cis	lymphoblastoid	seeQTL
rs2999528	THEM4	cis	uninvolved skin	skin_eQTL
rs2999528	THEM4	cis	Esophagus Muscularis	GTEx
rs2999528	THEM4	cis	Nerve Tibial	GTEx
rs2999528	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs2999528	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs2999528	THEM4	cis	cerebellum	SCAN
rs2999528	S100A10	cis	lymphoblastoid	seeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151934600-151953400	Weak transcription	Psoas Muscle	Psoas
2	chr1:151941000-151953200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:151941000-151953200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:151941000-151953400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:151941000-151953400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr1:151941000-151954800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:151941200-151953000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr1:151941200-151955200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:151941600-151961200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:151941800-151953000	Weak transcription	Lung	lung
11	chr1:151941800-151953600	Weak transcription	Gastric	stomach
12	chr1:151941800-151956200	Weak transcription	Pancreas	Pancrea
13	chr1:151943000-151953000	Weak transcription	Spleen	Spleen
14	chr1:151945400-151953400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:151945600-151953000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:151945600-151953600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr1:151945600-151953800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:151945600-151953800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:151946000-151954800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:151946000-151954800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:151946200-151953000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:151946200-151953000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr1:151946200-151954800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:151946200-151954800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:151946200-151956200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:151946600-151957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:151946600-151958800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:151947600-151953400	Enhancers	Placenta Amnion	Placenta Amnion
29	chr1:151948000-151956200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr1:151948400-151955200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr1:151949000-151953400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:151949200-151963200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:151949400-151953200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:151949800-151953400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:151949800-151953600	Weak transcription	Liver	Liver
36	chr1:151949800-151954800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:151949800-151957200	Weak transcription	Stomach Mucosa	stomach
38	chr1:151950000-151953000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:151950000-151953400	Weak transcription	Esophagus	oesophagus
40	chr1:151950000-151953600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr1:151950000-151956600	Genic enhancers	A549	lung
42	chr1:151950400-151953800	Weak transcription	Right Ventricle	heart
43	chr1:151950600-151953000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:151950600-151954800	Weak transcription	Small Intestine	intestine
45	chr1:151950800-151954000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:151951000-151953000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:151951000-151961800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:151951200-151953000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:151951200-151953200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:151951200-151954800	Weak transcription	HepG2	liver

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