Variant report

Variant	rs6906241
Chromosome Location	chr6:5262712-5262713
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	FOSL1	chr6:5262555-5262951	K562	blood:	n/a	n/a
2	FOSL2	chr6:5262574-5262956	HepG2	liver:	n/a	n/a
3	FOS	chr6:5262697-5262829	MCF10A-Er-Src	breast:	n/a	n/a
4	GTF3C2	chr6:5262247-5262878	Hela-S3	cervix:	n/a	n/a
5	FOS	chr6:5262696-5262984	MCF10A-Er-Src	breast:	n/a	n/a
6	ATF3	chr6:5262710-5263007	K562	blood:	n/a	n/a
7	JUND	chr6:5262644-5262908	H1-hESC	embryonic stem cell:	n/a	chr6:5262790-5262801
8	RCOR1	chr6:5262693-5262771	K562	blood:	n/a	n/a
9	TCF7L2	chr6:5262656-5262835	Hela-S3	cervix:	n/a	n/a
10	JUND	chr6:5262647-5262917	HepG2	liver:	n/a	chr6:5262790-5262801
11	JUND	chr6:5262620-5262994	K562	blood:	n/a	chr6:5262790-5262801
12	FOS	chr6:5262662-5262845	MCF10A-Er-Src	breast:	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: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12190040	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12204340	0.80[ASN][1000 genomes]
rs12215806	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2145373	0.87[EUR][1000 genomes]
rs4141761	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4499975	0.87[EUR][1000 genomes]
rs4585611	0.89[EUR][1000 genomes]
rs4610609	0.84[EUR][1000 genomes]
rs744758	0.97[EUR][1000 genomes]
rs7775335	0.88[EUR][1000 genomes]
rs9328292	0.84[EUR][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
rs6906241	LYRM4	cis	Thyroid	GTEx

Chromatin state (count:114 , 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	chr6:5260200-5262800	Active TSS	H9 Cell Line	embryonic stem cell
18	chr6:5260200-5262800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:5260200-5262800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:5260200-5262800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:5260200-5262800	Active TSS	Colonic Mucosa	Colon
22	chr6:5260200-5262800	Active TSS	Fetal Intestine Small	intestine
23	chr6:5260200-5262800	Active TSS	Left Ventricle	heart
24	chr6:5260200-5263000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:5260200-5263200	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr6:5260400-5262800	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr6:5260400-5262800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:5260400-5262800	Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr6:5260400-5262800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:5260400-5262800	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr6:5260400-5262800	Active TSS	Fetal Intestine Large	intestine
32	chr6:5260400-5262800	Active TSS	Pancreas	Pancrea
33	chr6:5260400-5262800	Active TSS	GM12878-XiMat	blood
34	chr6:5260400-5262800	Active TSS	HMEC	breast
35	chr6:5260400-5262800	Active TSS	NHEK	skin
36	chr6:5260400-5263000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:5260400-5263000	Active TSS	Fetal Kidney	kidney
38	chr6:5260400-5263000	Active TSS	Right Ventricle	heart
39	chr6:5260400-5263000	Active TSS	Hela-S3	cervix
40	chr6:5260600-5262800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:5260600-5262800	Active TSS	NHLF	lung
42	chr6:5260600-5263000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:5261800-5263200	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr6:5262000-5262800	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr6:5262000-5263000	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr6:5262000-5263000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:5262000-5263000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr6:5262000-5263200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:5262200-5262800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr6:5262200-5262800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland

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