Variant report

Variant	rs1218585
Chromosome Location	chr1:154832661-154832662
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr1:154832089-154833412	GM18951	blood:	n/a	n/a
2	POLR2A	chr1:154831732-154833515	GM12892	blood:	n/a	n/a
3	POLR2A	chr1:154832100-154833297	GM10847	blood:	n/a	n/a
4	MEF2A	chr1:154832006-154833221	GM12878	blood:	n/a	chr1:154832377-154832388
5	RELA	chr1:154832127-154833346	GM12891	blood:	n/a	n/a
6	POU2F2	chr1:154832052-154833358	GM12891	blood:	n/a	chr1:154832906-154832915 chr1:154832419-154832426 chr1:154832391-154832409 chr1:154832417-154832427 chr1:154832396-154832404 chr1:154832418-154832427 chr1:154832416-154832428 chr1:154832415-154832430 chr1:154832904-154832918 chr1:154832395-154832409 chr1:154832396-154832403 chr1:154832417-154832427 chr1:154832395-154832406 chr1:154832390-154832411 chr1:154832395-154832406 chr1:154832416-154832430 chr1:154832395-154832405 chr1:154832394-154832404 chr1:154832907-154832914 chr1:154832395-154832404 chr1:154832416-154832429 chr1:154832392-154832407
7	STAT5A	chr1:154831325-154833441	GM12878	blood:	n/a	chr1:154832652-154832666 chr1:154832538-154832550
8	POLR2A	chr1:154831263-154833473	GM19099	blood:	n/a	n/a
9	MAZ	chr1:154832264-154833322	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:154831038-154833419	GM12878	blood:	n/a	n/a
11	EBF1	chr1:154832055-154833404	GM12878	blood:	n/a	chr1:154832974-154832985
12	EP300	chr1:154832247-154833444	GM12878	blood:	n/a	chr1:154833049-154833058
13	FOXM1	chr1:154832138-154833382	GM12878	blood:	n/a	n/a
14	RUNX3	chr1:154832042-154833500	GM12878	blood:	n/a	chr1:154832939-154832948
15	NFIC	chr1:154831990-154833411	GM12878	blood:	n/a	n/a
16	MTA3	chr1:154831744-154833490	GM12878	blood:	n/a	n/a
17	EBF1	chr1:154831785-154833414	GM12878	blood:	n/a	chr1:154832974-154832985
18	POLR2A	chr1:154831318-154833415	GM18505	blood:	n/a	n/a
19	POLR2A	chr1:154831351-154833435	GM15510	blood:	n/a	n/a
20	RELA	chr1:154832119-154833414	GM19099	blood:	n/a	n/a
21	SP1	chr1:154832642-154833347	GM12878	blood:	n/a	chr1:154833145-154833152
22	BHLHE40	chr1:154832212-154833393	GM12878	blood:	n/a	chr1:154833174-154833190
23	RELA	chr1:154832127-154833379	GM19193	blood:	n/a	n/a
24	IKZF1	chr1:154832204-154833319	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:154832017-154833391	GM12878	blood:	n/a	n/a
26	TCF12	chr1:154832266-154833404	GM12878	blood:	n/a	chr1:154832549-154832559 chr1:154833283-154833290
27	POLR2A	chr1:154832082-154833371	GM12891	blood:	n/a	n/a
28	RUNX3	chr1:154831953-154833436	GM12878	blood:	n/a	chr1:154832939-154832948
29	STAT3	chr1:154832148-154833336	GM12878	blood:	n/a	chr1:154832652-154832666 chr1:154832538-154832550
30	POU2F2	chr1:154832110-154833331	GM12878	blood:	n/a	chr1:154832906-154832915 chr1:154832419-154832426 chr1:154832391-154832409 chr1:154832417-154832427 chr1:154832396-154832404 chr1:154832418-154832427 chr1:154832416-154832428 chr1:154832415-154832430 chr1:154832904-154832918 chr1:154832395-154832409 chr1:154832396-154832403 chr1:154832417-154832427 chr1:154832395-154832406 chr1:154832390-154832411 chr1:154832395-154832406 chr1:154832416-154832430 chr1:154832395-154832405 chr1:154832394-154832404 chr1:154832907-154832914 chr1:154832395-154832404 chr1:154832416-154832429 chr1:154832392-154832407
31	POU2F2	chr1:154832209-154833032	GM12878	blood:	n/a	chr1:154832906-154832915 chr1:154832419-154832426 chr1:154832391-154832409 chr1:154832417-154832427 chr1:154832396-154832404 chr1:154832418-154832427 chr1:154832416-154832428 chr1:154832415-154832430 chr1:154832904-154832918 chr1:154832395-154832409 chr1:154832396-154832403 chr1:154832417-154832427 chr1:154832395-154832406 chr1:154832390-154832411 chr1:154832395-154832406 chr1:154832416-154832430 chr1:154832395-154832405 chr1:154832394-154832404 chr1:154832907-154832914 chr1:154832395-154832404 chr1:154832416-154832429 chr1:154832392-154832407
32	STAT5A	chr1:154832073-154833340	GM12878	blood:	n/a	chr1:154832652-154832666 chr1:154832538-154832550
33	SPI1	chr1:154832583-154833399	GM12878	blood:	n/a	chr1:154833047-154833060
34	RELA	chr1:154832133-154833400	GM15510	blood:	n/a	n/a
35	ELF1	chr1:154832329-154833349	GM12878	blood:	n/a	n/a
36	BATF	chr1:154832179-154833312	GM12878	blood:	n/a	chr1:154832343-154832352
37	POLR2A	chr1:154831409-154833465	GM18951	blood:	n/a	n/a
38	FOXM1	chr1:154832243-154833421	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:154831711-154833367	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:154831980-154833350	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:154831384-154833484	GM19193	blood:	n/a	n/a
42	YY1	chr1:154832158-154832767	GM12878	blood:	n/a	n/a
43	EP300	chr1:154832214-154833360	GM12878	blood:	n/a	chr1:154833049-154833058
44	POU2F2	chr1:154831989-154833359	GM12878	blood:	n/a	chr1:154832906-154832915 chr1:154832419-154832426 chr1:154832391-154832409 chr1:154832417-154832427 chr1:154832396-154832404 chr1:154832418-154832427 chr1:154832416-154832428 chr1:154832415-154832430 chr1:154832904-154832918 chr1:154832395-154832409 chr1:154832396-154832403 chr1:154832417-154832427 chr1:154832395-154832406 chr1:154832390-154832411 chr1:154832395-154832406 chr1:154832416-154832430 chr1:154832395-154832405 chr1:154832394-154832404 chr1:154832907-154832914 chr1:154832395-154832404 chr1:154832416-154832429 chr1:154832392-154832407
45	POLR2A	chr1:154831926-154833376	GM12892	blood:	n/a	n/a
46	EP300	chr1:154832310-154833278	GM12878	blood:	n/a	chr1:154833049-154833058
47	TBL1XR1	chr1:154832137-154833344	GM12878	blood:	n/a	n/a
48	NFIC	chr1:154832167-154833446	GM12878	blood:	n/a	n/a
49	YY1	chr1:154832368-154833340	GM12892	blood:	n/a	n/a
50	PAX5	chr1:154832138-154833478	GM12878	blood:	n/a	chr1:154833048-154833057

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154771337..154773585-chr1:154832415..154834960,2	MCF-7	breast:

Variant related genes	Relation type
KCNN3	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1061122	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908443	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11264302	1.00[JPT][hapmap]
rs11264303	1.00[JPT][hapmap]
rs11582128	1.00[JPT][hapmap]
rs1218554	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1218584	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1218587	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1218588	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1218589	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1218592	1.00[ASN][1000 genomes]
rs12760148	1.00[CHB][hapmap]
rs16836525	1.00[CHB][hapmap]
rs2878412	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845396	1.00[CHB][hapmap]
rs4845397	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4845402	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4845675	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6660884	1.00[JPT][hapmap]
rs6682335	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs906596	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs906597	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv432931	chr1:154794318-154855055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	esv29982	chr1:154818353-154882544	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv432942	chr1:154818353-154903047	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv432964	chr1:154820067-154849590	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv432953	chr1:154820067-154855055	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1218585	C1orf85	cis	parietal	SCAN
rs1218585	S100A7L2	cis	parietal	SCAN
rs1218585	LENEP	cis	cerebellum	SCAN
rs1218585	PSMD4	cis	cerebellum	SCAN
rs1218585	BCAN	cis	parietal	SCAN
rs1218585	INTS3	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154821000-154837200	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:154822600-154838000	Weak transcription	Brain Angular Gyrus	brain
3	chr1:154824400-154834200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:154827600-154839400	Enhancers	Fetal Brain Male	brain
5	chr1:154827800-154833600	Enhancers	Fetal Muscle Leg	muscle
6	chr1:154828000-154833400	Enhancers	Brain Anterior Caudate	brain
7	chr1:154828400-154833400	Flanking Active TSS	GM12878-XiMat	blood
8	chr1:154829200-154833000	Weak transcription	Brain Substantia Nigra	brain
9	chr1:154830400-154832800	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr1:154830600-154833400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr1:154830800-154834000	Strong transcription	Fetal Stomach	stomach
12	chr1:154831200-154839800	Enhancers	Psoas Muscle	Psoas
13	chr1:154831400-154839400	Enhancers	Primary B cells from peripheral blood	blood
14	chr1:154831600-154832800	Active TSS	Duodenum Mucosa	Duodenum
15	chr1:154831600-154833000	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr1:154831600-154833400	Enhancers	Brain Germinal Matrix	brain
17	chr1:154831600-154835200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:154831800-154832800	Enhancers	Brain Cingulate Gyrus	brain
19	chr1:154831800-154833400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr1:154831800-154833400	Enhancers	Right Ventricle	heart
21	chr1:154831800-154835800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr1:154831800-154839400	Enhancers	Fetal Thymus	thymus
23	chr1:154832000-154833000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:154832000-154833000	Enhancers	Spleen	Spleen
25	chr1:154832000-154833200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:154832000-154833200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr1:154832000-154834400	Enhancers	Thymus	Thymus
28	chr1:154832000-154834800	Enhancers	Primary B cells from cord blood	blood
29	chr1:154832000-154837000	Enhancers	HSMM	muscle
30	chr1:154832200-154832800	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr1:154832200-154832800	Weak transcription	Colonic Mucosa	Colon
32	chr1:154832200-154832800	Enhancers	HMEC	breast
33	chr1:154832200-154833000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:154832200-154834200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:154832200-154836600	Enhancers	Muscle Satellite Cultured Cells	--
36	chr1:154832400-154832800	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr1:154832400-154832800	Flanking Active TSS	HSMMtube	muscle
38	chr1:154832400-154832800	Enhancers	NHEK	skin
39	chr1:154832400-154833000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:154832400-154833000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:154832400-154833000	Enhancers	Brain Hippocampus Middle	brain
42	chr1:154832400-154833000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:154832400-154833200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:154832400-154833200	Enhancers	Left Ventricle	heart
45	chr1:154832400-154834000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:154832400-154834600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:154832400-154840000	Enhancers	K562	blood
48	chr1:154832600-154832800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr1:154832600-154832800	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr1:154832600-154832800	Enhancers	HUES6 Cell Line	embryonic stem cell

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