Variant report

Variant	rs6925249
Chromosome Location	chr6:5262510-5262511
allele	G/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	POLR2A	chr6:5260212-5262541	GM12891	blood:	n/a	n/a
2	YY1	chr6:5262506-5262658	K562	blood:	n/a	n/a
3	HCFC1	chr6:5259374-5262547	Hela-S3	cervix:	n/a	n/a
4	MXI1	chr6:5259910-5262664	SK-N-SH	brain:	n/a	chr6:5261474-5261489
5	POLR2A	chr6:5260367-5262627	GM12892	blood:	n/a	n/a
6	PAX5	chr6:5262228-5262526	GM12891	blood:	n/a	chr6:5262414-5262423
7	GTF3C2	chr6:5262247-5262878	Hela-S3	cervix:	n/a	n/a
8	MXI1	chr6:5259637-5262620	IMR90	lung:	n/a	chr6:5261474-5261489
9	POLR2A	chr6:5262407-5262541	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5262260..5264033-chr6:5288601..5290275,2	K562	blood:

Variant related genes	Relation type
LYRM4	TF binding region

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs12174086	0.83[ASN][1000 genomes]
rs13191012	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1570085	0.99[ASN][1000 genomes]
rs1609808	0.97[ASN][1000 genomes]
rs17139985	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2145372	0.97[ASN][1000 genomes]
rs2224391	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2224392	0.99[ASN][1000 genomes]
rs2753222	0.93[ASN][1000 genomes]
rs2753223	0.97[ASN][1000 genomes]
rs2753224	0.97[ASN][1000 genomes]
rs2753228	0.97[ASN][1000 genomes]
rs2753229	0.97[ASN][1000 genomes]
rs2753230	0.97[ASN][1000 genomes]
rs2753233	0.99[ASN][1000 genomes]
rs2753234	0.99[ASN][1000 genomes]
rs2753235	0.98[ASN][1000 genomes]
rs2753236	0.83[ASN][1000 genomes]
rs2753237	0.99[ASN][1000 genomes]
rs2753238	0.98[ASN][1000 genomes]
rs2753239	0.99[ASN][1000 genomes]
rs2753240	0.99[ASN][1000 genomes]
rs2753243	0.97[ASN][1000 genomes]
rs2753244	0.99[ASN][1000 genomes]
rs2753245	0.99[ASN][1000 genomes]
rs2753246	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2753247	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2753248	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2753249	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773296	0.82[ASN][1000 genomes]
rs2773298	0.93[ASN][1000 genomes]
rs2773299	0.94[ASN][1000 genomes]
rs2773300	0.93[ASN][1000 genomes]
rs2773302	0.96[ASN][1000 genomes]
rs2773304	0.95[ASN][1000 genomes]
rs2773306	0.97[ASN][1000 genomes]
rs2773307	0.97[ASN][1000 genomes]
rs2773308	0.97[ASN][1000 genomes]
rs2773309	0.86[ASN][1000 genomes]
rs2773310	0.99[ASN][1000 genomes]
rs2773311	0.99[ASN][1000 genomes]
rs2773312	0.99[ASN][1000 genomes]
rs2773314	0.99[ASN][1000 genomes]
rs2773316	0.99[ASN][1000 genomes]
rs2773317	0.99[ASN][1000 genomes]
rs2773318	0.99[ASN][1000 genomes]
rs2773319	0.99[ASN][1000 genomes]
rs2773320	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773322	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35048711	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36055504	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6909619	0.99[ASN][1000 genomes]
rs6913120	0.99[ASN][1000 genomes]
rs766339	0.97[ASN][1000 genomes]
rs766340	0.97[ASN][1000 genomes]
rs7752203	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7758400	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs928170	0.99[ASN][1000 genomes]
rs9328289	0.81[ASN][1000 genomes]
rs9378420	0.89[ASN][1000 genomes]
rs9378943	0.82[ASN][1000 genomes]
rs9392665	0.91[ASN][1000 genomes]
rs9392666	0.99[ASN][1000 genomes]
rs9405259	0.80[ASN][1000 genomes]
rs9405260	0.91[ASN][1000 genomes]
rs9405809	0.89[ASN][1000 genomes]
rs9405811	0.94[ASN][1000 genomes]
rs9405813	0.89[ASN][1000 genomes]
rs9504364	0.99[ASN][1000 genomes]
rs9504365	0.99[ASN][1000 genomes]
rs9504368	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9504369	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504371	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9784870	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1021646	chr6:5157795-5367254	Enhancers Flanking Active TSS Active TSS Weak transcription Strong 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	8 gene(s)	inside rSNPs	diseases
11	nsv538115	chr6:5157795-5367254	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1029609	chr6:5187633-5397254	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1035080	chr6:5206533-5396019	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv538116	chr6:5206533-5396019	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv1016456	chr6:5216835-5315913	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv538117	chr6:5216835-5315913	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS 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	10 gene(s)	inside rSNPs	diseases
19	nsv1028185	chr6:5247624-5340163	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6925249	LYRM4	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5259600-5263000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:5259600-5263200	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr6:5259800-5262800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:5259800-5262800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:5259800-5263200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr6:5260000-5262800	Active TSS	A549	lung
7	chr6:5260000-5262800	Active TSS	NHDF-Ad	bronchial
8	chr6:5260000-5263000	Active TSS	H1 Cell Line	embryonic stem cell
9	chr6:5260000-5263000	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr6:5260000-5263000	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr6:5260000-5263000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:5260000-5263000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:5260000-5263000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:5260000-5263200	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr6:5260000-5263200	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr6:5260000-5263200	Active TSS	K562	blood
17	chr6:5260200-5262600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr6:5260200-5262600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:5260200-5262600	Active TSS	Esophagus	oesophagus
20	chr6:5260200-5262600	Active TSS	Ovary	ovary
21	chr6:5260200-5262800	Active TSS	H9 Cell Line	embryonic stem cell
22	chr6:5260200-5262800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:5260200-5262800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:5260200-5262800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:5260200-5262800	Active TSS	Colonic Mucosa	Colon
26	chr6:5260200-5262800	Active TSS	Fetal Intestine Small	intestine
27	chr6:5260200-5262800	Active TSS	Left Ventricle	heart
28	chr6:5260200-5263000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:5260200-5263200	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr6:5260400-5262600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:5260400-5262600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:5260400-5262600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:5260400-5262600	Active TSS	Muscle Satellite Cultured Cells	--
34	chr6:5260400-5262600	Active TSS	Colon Smooth Muscle	Colon
35	chr6:5260400-5262600	Active TSS	Fetal Heart	heart
36	chr6:5260400-5262600	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr6:5260400-5262600	Active TSS	Fetal Lung	lung
38	chr6:5260400-5262600	Active TSS	Fetal Stomach	stomach
39	chr6:5260400-5262600	Active TSS	Psoas Muscle	Psoas
40	chr6:5260400-5262600	Active TSS	Stomach Mucosa	stomach
41	chr6:5260400-5262800	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr6:5260400-5262800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:5260400-5262800	Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr6:5260400-5262800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:5260400-5262800	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr6:5260400-5262800	Active TSS	Fetal Intestine Large	intestine
47	chr6:5260400-5262800	Active TSS	Pancreas	Pancrea
48	chr6:5260400-5262800	Active TSS	GM12878-XiMat	blood
49	chr6:5260400-5262800	Active TSS	HMEC	breast
50	chr6:5260400-5262800	Active TSS	NHEK	skin

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