Variant report

Variant	rs585956
Chromosome Location	chr6:5135156-5135157
allele	C/T
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	NR3C1	chr6:5135116-5135780	A549	lung:	n/a	n/a

Variant related genes	Relation type
LYRM4	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs127124	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs127125	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs364886	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs412628	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs423801	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs454984	0.83[ASN][1000 genomes]
rs455803	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs457846	0.81[ASN][1000 genomes]
rs464606	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs464863	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs585970	0.81[ASN][1000 genomes]
rs73717674	0.84[AFR][1000 genomes]
rs85204	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 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
15	esv3390320	chr6:5134378-5136926	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv2469123	chr6:5134492-5136200	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv3401138	chr6:5134553-5136701	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	esv1953097	chr6:5135041-5135836	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	esv3377438	chr6:5135043-5135899	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	esv3364199	chr6:5135057-5135869	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	esv3490609	chr6:5135072-5135905	Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	esv3472038	chr6:5135093-5135821	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	esv3472039	chr6:5135093-5135821	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	esv3490610	chr6:5135130-5135606	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
25	nsv600874	chr6:5135156-5135675	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
26	nsv600875	chr6:5135156-5135726	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	nsv600876	chr6:5135156-5135776	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	nsv600877	chr6:5135156-5135777	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	nsv600878	chr6:5135156-5135969	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs585956	LYRM4	cis	multi-tissue	Pritchard
rs585956	LYRM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5128800-5136200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr6:5129000-5136800	Weak transcription	Primary T cells from cord blood	blood
3	chr6:5129000-5162000	Weak transcription	K562	blood
4	chr6:5129800-5138000	Weak transcription	HepG2	liver
5	chr6:5130600-5140400	Weak transcription	Gastric	stomach
6	chr6:5130600-5172200	Weak transcription	Lung	lung
7	chr6:5130800-5139400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:5130800-5142400	Weak transcription	Fetal Intestine Small	intestine
9	chr6:5131000-5143000	Weak transcription	Spleen	Spleen
10	chr6:5131800-5135200	Weak transcription	Placenta	Placenta
11	chr6:5132000-5139200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:5133200-5141800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:5133400-5135200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr6:5133400-5136600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:5133400-5143200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:5133400-5143800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:5133400-5144000	Weak transcription	Fetal Brain Male	brain
18	chr6:5133400-5146000	Weak transcription	Psoas Muscle	Psoas
19	chr6:5133400-5151600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:5133600-5136600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:5133600-5143400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:5133600-5143800	Weak transcription	Fetal Stomach	stomach
23	chr6:5133800-5136200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:5133800-5136200	Weak transcription	Brain Anterior Caudate	brain
25	chr6:5133800-5136200	Weak transcription	HUVEC	blood vessel
26	chr6:5133800-5139200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr6:5133800-5139400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:5133800-5140000	Weak transcription	GM12878-XiMat	blood
29	chr6:5133800-5140600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:5133800-5142400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:5133800-5143000	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:5133800-5143400	Weak transcription	Left Ventricle	heart
33	chr6:5133800-5143600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:5133800-5153400	Weak transcription	Right Ventricle	heart
35	chr6:5134000-5135800	Enhancers	NHEK	skin
36	chr6:5134200-5135800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:5134200-5139000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:5134200-5144200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr6:5134400-5135600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:5134400-5136000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr6:5134400-5139000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:5134400-5139000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr6:5134600-5136200	Weak transcription	Adipose Nuclei	Adipose
44	chr6:5134600-5138800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:5134600-5139000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:5134600-5139000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:5134800-5135800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:5135000-5135200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:5135000-5151000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links