Variant report

Variant	rs56019796
Chromosome Location	chr7:150009226-150009227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:150008263..150011121-chr7:150102492..150104771,2	K562	blood:
2	chr7:150005819..150007873-chr7:150009129..150011102,2	K562	blood:
3	chr7:150007648..150010098-chr7:150018612..150020930,2	MCF-7	breast:
4	chr7:150009132..150011651-chr7:150053831..150057388,3	K562	blood:

Variant related genes	Relation type
ENSG00000106526	Chromatin interaction
ENSG00000196456	Chromatin interaction
ENSG00000127399	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10952249	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10952250	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11764936	0.85[EUR][1000 genomes]
rs11765644	0.85[EUR][1000 genomes]
rs11765692	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11766288	0.90[EUR][1000 genomes]
rs11767726	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11769348	0.85[EUR][1000 genomes]
rs11773351	0.83[EUR][1000 genomes]
rs11974980	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11975886	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11983355	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1464752	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1464753	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17837498	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1916932	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1962004	0.88[EUR][1000 genomes]
rs1983440	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2108851	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2108852	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2108853	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2108854	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2159234	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2159235	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2159236	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2373751	0.85[EUR][1000 genomes]
rs3088207	0.83[EUR][1000 genomes]
rs3735169	0.83[EUR][1000 genomes]
rs3735170	0.83[EUR][1000 genomes]
rs3735171	0.84[EUR][1000 genomes]
rs3735172	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3735173	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3735174	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3735175	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3800780	0.85[EUR][1000 genomes]
rs3800781	0.85[EUR][1000 genomes]
rs4395803	0.85[EUR][1000 genomes]
rs4554381	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55715989	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55881542	0.85[EUR][1000 genomes]
rs56190213	0.85[EUR][1000 genomes]
rs56402329	0.81[EUR][1000 genomes]
rs56923535	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56998970	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57888387	0.92[EUR][1000 genomes]
rs59572505	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60268791	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60283368	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60467296	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73170169	0.92[EUR][1000 genomes]
rs73170174	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73170185	0.85[EUR][1000 genomes]
rs7781827	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7788316	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7806429	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889435	chr7:149585379-150013393	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv1015582	chr7:149967986-150285104	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv981608	chr7:150002640-150009746	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv508490	chr7:150006068-150051241	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs56019796	LRRC61	cis	Esophagus Mucosa	GTEx
rs56019796	LRRC61	cis	Muscle Skeletal	GTEx
rs56019796	LRRC61	Cis_1M	lymphoblastoid	RTeQTL
rs56019796	REPIN1	cis	Muscle Skeletal	GTEx
rs56019796	C7orf29	Cis_1M	lymphoblastoid	RTeQTL
rs56019796	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx
rs56019796	LRRC61	cis	Whole Blood	GTEx
rs56019796	ZBED6CL	cis	Esophagus Mucosa	GTEx
rs56019796	ZBED6CL	cis	Esophagus Muscularis	GTEx
rs56019796	RARRES2	cis	multi-tissue	Pritchard
rs56019796	LRRC61	cis	Heart Left Ventricle	GTEx
rs56019796	LRRC61	cis	Thyroid	GTEx
rs56019796	LRRC61	cis	Nerve Tibial	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:149984200-150012400	Weak transcription	Liver	Liver
2	chr7:149984200-150019400	Weak transcription	Colonic Mucosa	Colon
3	chr7:149992400-150018000	Weak transcription	Fetal Intestine Small	intestine
4	chr7:150003800-150016000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:150004000-150019000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr7:150005200-150010000	Weak transcription	HepG2	liver
7	chr7:150007000-150010200	Enhancers	Hela-S3	cervix
8	chr7:150007000-150015000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:150007600-150018000	Weak transcription	Fetal Intestine Large	intestine
10	chr7:150008000-150010400	Enhancers	Fetal Muscle Leg	muscle
11	chr7:150008400-150009600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:150008400-150010200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr7:150008400-150010400	Enhancers	HSMMtube	muscle
14	chr7:150008400-150011200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:150008600-150011000	Weak transcription	Gastric	stomach
16	chr7:150008800-150009400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:150008800-150009600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr7:150008800-150009800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
19	chr7:150008800-150010600	Enhancers	HSMM	muscle
20	chr7:150008800-150011400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
21	chr7:150008800-150011600	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr7:150008800-150011600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
23	chr7:150009000-150009400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr7:150009000-150009400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
25	chr7:150009000-150009400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr7:150009000-150009600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:150009000-150009600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr7:150009000-150009800	Enhancers	NH-A	brain
29	chr7:150009000-150010000	Weak transcription	Pancreas	Pancrea
30	chr7:150009000-150010200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:150009000-150010400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr7:150009000-150010400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr7:150009000-150010600	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr7:150009000-150011400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr7:150009200-150009400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr7:150009200-150009600	Enhancers	H9 Cell Line	embryonic stem cell
37	chr7:150009200-150009600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr7:150009200-150009800	Flanking Active TSS	K562	blood
39	chr7:150009200-150010000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr7:150009200-150010200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr7:150009200-150010200	Weak transcription	Fetal Kidney	kidney
42	chr7:150009200-150010800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr7:150009200-150011000	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr7:150009200-150011000	Weak transcription	Spleen	Spleen
45	chr7:150009200-150011400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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