Variant report

Variant	rs85204
Chromosome Location	chr6:5133432-5133433
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:5133266-5133448	GM19240	blood:	n/a	n/a
2	CTCF	chr6:5133320-5133470	NHLF	lung:	n/a	n/a
3	CTCF	chr6:5133300-5133450	AG04450	lung:	n/a	n/a
4	CTCF	chr6:5133360-5133510	GM12872	blood:	n/a	n/a
5	CTCF	chr6:5133320-5133470	GM12872	blood:	n/a	n/a
6	CTCF	chr6:5133320-5133470	HPF	lung:	n/a	n/a
7	CTCF	chr6:5133202-5133557	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:5132693-5133514	GM12892	blood:	n/a	n/a
9	CTCF	chr6:5133320-5133470	GM12874	blood:	n/a	n/a
10	CTCF	chr6:5133285-5133619	MCF-7	breast:	n/a	n/a
11	CTCF	chr6:5133340-5133490	GM12864	blood:	n/a	n/a
12	EBF1	chr6:5133032-5133515	GM12878	blood:	n/a	chr6:5133265-5133276
13	CTCF	chr6:5133270-5133434	Fibrobl	skin:	n/a	n/a
14	CTCF	chr6:5133303-5133452	MCF-7	breast:	n/a	n/a
15	CTCF	chr6:5133293-5133443	MCF-7	breast:	n/a	n/a
16	CREB1	chr6:5132912-5133437	GM12878	blood:	n/a	n/a
17	CTCF	chr6:5133320-5133470	GM12864	blood:	n/a	n/a
18	CTCF	chr6:5133338-5133448	GM13977	blood:	n/a	n/a
19	CTCF	chr6:5133320-5133470	GM12865	blood:	n/a	n/a
20	POLR2A	chr6:5132858-5134054	IMR90	lung:	n/a	n/a
21	CTCF	chr6:5133297-5133440	GM12891	blood:	n/a	n/a
22	CTCF	chr6:5133300-5133450	GM12867	blood:	n/a	n/a
23	CTCF	chr6:5133300-5133450	GM12872	blood:	n/a	n/a
24	CTCF	chr6:5133160-5133450	GM06990	blood:	n/a	n/a
25	CTCF	chr6:5133300-5133450	GM12873	blood:	n/a	n/a
26	CTCF	chr6:5133271-5133462	MCF-7	breast:	n/a	n/a
27	POLR2A	chr6:5132688-5133531	GM12892	blood:	n/a	n/a
28	POLR2A	chr6:5132778-5133439	GM12892	blood:	n/a	n/a
29	CTCF	chr6:5133309-5133446	Lung_OC	lung:	n/a	n/a
30	RAD21	chr6:5132896-5133525	IMR90	lung:	n/a	n/a
31	CTCF	chr6:5133300-5133450	GM06990	blood:	n/a	n/a
32	CTCF	chr6:5133309-5133461	MCF-7	breast:	n/a	n/a
33	CTCF	chr6:5133283-5133448	MCF-7	breast:	n/a	n/a
34	CTCF	chr6:5133326-5133459	GM10266	blood:	n/a	n/a
35	CTCF	chr6:5133260-5133452	GM19238	blood:	n/a	n/a
36	CTCF	chr6:5133380-5133530	GM12873	blood:	n/a	n/a
37	CTCF	chr6:5133237-5133454	GM19239	blood:	n/a	n/a
38	CTCF	chr6:5133320-5133470	HCM	heart:	n/a	n/a
39	CTCF	chr6:5133320-5133470	HCFaa	heart:	n/a	n/a
40	CTCF	chr6:5133251-5133457	GM12892	blood:	n/a	n/a
41	PAX5	chr6:5132915-5133485	GM12878	blood:	n/a	n/a
42	CTCF	chr6:5133312-5133451	GM12878	blood:	n/a	n/a

No data

Variant related genes	Relation type
LYRM4	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11242992	0.82[CEU][hapmap]
rs127124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs127125	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs200863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs364886	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs373696	1.00[MEX][hapmap]
rs385315	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs402541	0.88[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs412628	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs423801	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs435175	0.84[ASN][1000 genomes]
rs438298	0.82[ASN][1000 genomes]
rs445204	0.89[ASN][1000 genomes]
rs454984	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs455803	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs457453	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs457846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs458395	0.86[CEU][hapmap];0.89[JPT][hapmap]
rs460416	0.95[MEX][hapmap]
rs461698	0.86[ASN][1000 genomes]
rs462749	0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs464606	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464681	0.94[CHB][hapmap];0.85[CHD][hapmap];0.86[ASN][1000 genomes]
rs464863	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs466837	0.90[ASN][1000 genomes]
rs4959328	0.82[CEU][hapmap]
rs4960067	0.81[CEU][hapmap]
rs585956	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs585970	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs587777	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs683261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6914985	0.82[CEU][hapmap]
rs73717674	0.94[AFR][1000 genomes]
rs9504338	0.82[CEU][hapmap]
rs9606	0.88[CHB][hapmap];0.85[CHD][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
8	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1017821	chr6:5114609-5213200	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
12	nsv538114	chr6:5114609-5213200	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
13	nsv5179	chr6:5121824-5167027	Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs85204	LYRM4	cis	cerebellum	SCAN
rs85204	C6orf149	cis	multi-tissue	Pritchard

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5126600-5134000	Weak transcription	NHEK	skin
2	chr6:5128800-5136200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr6:5129000-5136800	Weak transcription	Primary T cells from cord blood	blood
4	chr6:5129000-5162000	Weak transcription	K562	blood
5	chr6:5129800-5138000	Weak transcription	HepG2	liver
6	chr6:5130600-5140400	Weak transcription	Gastric	stomach
7	chr6:5130600-5172200	Weak transcription	Lung	lung
8	chr6:5130800-5139400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:5130800-5142400	Weak transcription	Fetal Intestine Small	intestine
10	chr6:5131000-5143000	Weak transcription	Spleen	Spleen
11	chr6:5131400-5133800	Enhancers	Brain Cingulate Gyrus	brain
12	chr6:5131600-5133800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:5131800-5134400	Enhancers	Primary B cells from peripheral blood	blood
14	chr6:5131800-5135200	Weak transcription	Placenta	Placenta
15	chr6:5132000-5133600	Enhancers	Fetal Stomach	stomach
16	chr6:5132000-5133800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:5132000-5133800	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr6:5132000-5134600	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr6:5132000-5139200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:5132200-5133600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:5132200-5133600	Active TSS	Right Atrium	heart
22	chr6:5132200-5133800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr6:5132200-5134400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr6:5132200-5134400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr6:5132400-5133600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr6:5132400-5133600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:5132400-5133600	Enhancers	Colon Smooth Muscle	Colon
28	chr6:5132400-5133800	Enhancers	H1 Cell Line	embryonic stem cell
29	chr6:5132600-5133600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr6:5132600-5133600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:5132600-5133600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:5132600-5133600	Flanking Active TSS	GM12878-XiMat	blood
33	chr6:5132600-5134600	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr6:5132800-5133600	Enhancers	HSMMtube	muscle
35	chr6:5132800-5133800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr6:5133000-5133600	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr6:5133000-5134200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:5133000-5134400	Enhancers	H9 Cell Line	embryonic stem cell
39	chr6:5133200-5133600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:5133200-5133600	Enhancers	Osteobl	bone
41	chr6:5133200-5133800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:5133200-5133800	Enhancers	Right Ventricle	heart
43	chr6:5133200-5141800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:5133400-5133600	Enhancers	Stomach Smooth Muscle	stomach
45	chr6:5133400-5133800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:5133400-5133800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:5133400-5133800	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr6:5133400-5133800	Enhancers	Brain Substantia Nigra	brain
49	chr6:5133400-5133800	Enhancers	Fetal Muscle Leg	muscle
50	chr6:5133400-5133800	Enhancers	Left Ventricle	heart

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