Variant report

Variant	rs9791263
Chromosome Location	chr6:5175296-5175297
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5143652..5144542-chr6:5175040..5175982,3	MCF-7	breast:
2	chr6:5173898..5177005-chr6:5178469..5180479,3	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10458086	0.82[JPT][hapmap]
rs10498665	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11242995	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12190412	0.86[JPT][hapmap]
rs12660749	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs2143692	0.83[CHB][hapmap];0.87[JPT][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41302851	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4144009	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4959336	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62385012	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6901828	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6934882	0.86[JPT][hapmap]
rs7740952	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7763280	0.82[JPT][hapmap]
rs7764853	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
9	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
10	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
11	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
12	nsv1022336	chr6:5145194-5200687	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1018984	chr6:5145194-5200801	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
14	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
15	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9791263	LYRM4	cis	Thyroid	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5144000-5175400	Weak transcription	HepG2	liver
2	chr6:5145400-5180800	Weak transcription	Fetal Intestine Small	intestine
3	chr6:5153200-5178200	Weak transcription	HMEC	breast
4	chr6:5163800-5177600	Weak transcription	Aorta	Aorta
5	chr6:5163800-5189600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:5170400-5181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:5172200-5176200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:5172400-5175800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:5173000-5185400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:5173000-5190800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:5173200-5186000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:5173600-5175400	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:5173600-5181000	Weak transcription	NHEK	skin
14	chr6:5173800-5179800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr6:5174000-5175600	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr6:5174000-5176200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr6:5174000-5179800	Enhancers	Fetal Thymus	thymus
18	chr6:5174000-5181000	Weak transcription	Pancreas	Pancrea
19	chr6:5174200-5175400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr6:5174200-5175600	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr6:5174200-5175600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr6:5174400-5175400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr6:5174400-5175400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:5174400-5175400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:5174400-5175600	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr6:5174400-5175600	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr6:5174400-5176000	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr6:5174600-5175400	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr6:5174600-5175400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:5174600-5176200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:5174600-5176200	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr6:5174800-5175400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:5174800-5175800	Enhancers	Fetal Lung	lung
34	chr6:5174800-5176200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:5174800-5176200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:5174800-5176200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:5174800-5176200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr6:5174800-5176800	Enhancers	Primary B cells from peripheral blood	blood
39	chr6:5174800-5176800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:5174800-5176800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:5174800-5180600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:5175000-5175400	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr6:5175000-5175400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:5175000-5175400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr6:5175000-5175400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr6:5175000-5175400	Flanking Active TSS	Brain Substantia Nigra	brain
47	chr6:5175000-5175400	Flanking Active TSS	Dnd41	blood
48	chr6:5175000-5175400	Enhancers	Osteobl	bone
49	chr6:5175000-5175600	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr6:5175000-5175600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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