Variant report

Variant	rs11242993
Chromosome Location	chr6:5130232-5130233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:5120295..5122743-chr6:5128225..5130886,2	K562	blood:
2	chr6:5120935..5125341-chr6:5126554..5131441,5	K562	blood:
3	chr6:5127863..5130262-chr6:5130586..5132719,2	K562	blood:
4	chr6:5128862..5130386-chr6:5130746..5132624,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10458182	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10484846	0.82[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11242990	0.83[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11242991	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12110634	0.89[CEU][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12111219	0.88[CEU][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12191255	0.88[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12192863	0.94[CEU][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12193229	0.82[EUR][1000 genomes]
rs12195956	0.88[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12202160	0.87[CEU][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12202384	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12203248	0.82[EUR][1000 genomes]
rs12204382	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12204490	0.89[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12206931	0.87[CEU][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12213584	0.82[EUR][1000 genomes]
rs13194957	0.89[CEU][hapmap];0.95[YRI][hapmap]
rs17139439	0.88[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35400671	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs392847	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs417629	0.80[AFR][1000 genomes]
rs425930	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs455303	0.87[ASN][1000 genomes]
rs460111	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs466906	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs467373	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4959330	0.80[EUR][1000 genomes]
rs4959331	0.80[EUR][1000 genomes]
rs4960066	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4960068	0.80[EUR][1000 genomes]
rs6597114	0.94[CEU][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6597115	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6911123	0.89[EUR][1000 genomes]
rs72811642	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72811643	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs761365	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7757651	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9405800	0.94[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9405801	0.94[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9502267	0.80[ASN][1000 genomes]
rs9502269	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9504328	0.83[ASN][1000 genomes]
rs9504329	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9504339	0.93[ASN][1000 genomes]
rs9504341	0.93[ASN][1000 genomes]
rs9504350	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9504351	1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11242993	LYRM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5101800-5132200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr6:5103200-5132800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:5105200-5131400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:5107800-5132000	Weak transcription	Pancreas	Pancrea
5	chr6:5112800-5132600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr6:5113000-5130400	Weak transcription	Gastric	stomach
7	chr6:5113200-5130400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr6:5113400-5132400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:5123200-5130400	Weak transcription	Left Ventricle	heart
10	chr6:5123400-5132200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:5124800-5133200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:5125000-5130600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:5125000-5133200	Weak transcription	Right Ventricle	heart
14	chr6:5126400-5131800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:5126600-5130400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:5126600-5130400	Weak transcription	Right Atrium	heart
17	chr6:5126600-5133200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:5126600-5134000	Weak transcription	NHEK	skin
19	chr6:5126800-5130400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:5126800-5131600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:5126800-5132000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:5126800-5132000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:5126800-5132200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr6:5126800-5132200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:5126800-5132200	Weak transcription	Ovary	ovary
26	chr6:5126800-5132800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:5127000-5130600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:5127000-5131400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr6:5127000-5132200	Weak transcription	NHDF-Ad	bronchial
30	chr6:5127200-5132600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:5127600-5130400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:5128600-5131000	Enhancers	Spleen	Spleen
33	chr6:5128600-5132400	Weak transcription	Primary B cells from cord blood	blood
34	chr6:5128800-5130600	Weak transcription	Placenta	Placenta
35	chr6:5128800-5132400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr6:5128800-5136200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr6:5129000-5130800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:5129000-5130800	Strong transcription	Fetal Intestine Small	intestine
39	chr6:5129000-5136800	Weak transcription	Primary T cells from cord blood	blood
40	chr6:5129000-5162000	Weak transcription	K562	blood
41	chr6:5129200-5130600	Enhancers	Lung	lung
42	chr6:5129200-5132600	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr6:5129600-5130400	Weak transcription	Fetal Stomach	stomach
44	chr6:5129800-5131800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr6:5129800-5138000	Weak transcription	HepG2	liver
46	chr6:5130000-5130800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:5130000-5131000	Enhancers	Fetal Heart	heart
48	chr6:5130000-5132600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:5130200-5130600	Weak transcription	Brain Anterior Caudate	brain
50	chr6:5130200-5130800	Flanking Active TSS	Adipose Nuclei	Adipose

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