Variant report

Variant	rs11978339
Chromosome Location	chr7:102993026-102993027
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	POLR2A	chr7:102992916-102993137	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:102991625..102994191-chr7:102997426..102999083,2	K562	blood:
2	chr7:102991838..102993552-chr7:103006379..103009024,2	MCF-7	breast:

Variant related genes	Relation type
PSMC2	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10245155	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10257369	0.93[CEU][hapmap]
rs10266523	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10268808	0.88[CEU][hapmap]
rs10271758	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10486853	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs17136078	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs17136079	0.88[CEU][hapmap]
rs17136083	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs17136728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17606134	0.82[JPT][hapmap]
rs17680523	1.00[JPT][hapmap]
rs17837510	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs1861731	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs1968201	0.82[JPT][hapmap]
rs2193420	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs2878	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3087615	1.00[JPT][hapmap]
rs4266582	0.88[CEU][hapmap]
rs4593456	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs4727563	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs4727566	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs4729887	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs4729891	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs4729896	0.94[CEU][hapmap];0.82[JPT][hapmap]
rs4729899	0.88[CEU][hapmap]
rs4729902	0.88[CEU][hapmap]
rs5025411	0.82[JPT][hapmap]
rs62481648	0.82[EUR][1000 genomes]
rs62481655	0.88[EUR][1000 genomes]
rs62482371	0.88[EUR][1000 genomes]
rs62482396	0.98[EUR][1000 genomes]
rs62482404	1.00[ASN][1000 genomes]
rs62482405	0.96[ASN][1000 genomes]
rs62482406	1.00[ASN][1000 genomes]
rs6971734	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6972190	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73175852	0.96[ASN][1000 genomes]
rs7455141	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs7777392	0.88[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs7804020	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030446	chr7:102932689-103221638	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv491911	chr7:102967150-103403622	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11978339	RP11-401L13.5	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102988600-103002400	Weak transcription	Spleen	Spleen
2	chr7:102989000-103006200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:102989200-102993200	Weak transcription	Aorta	Aorta
4	chr7:102989200-102994800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:102989200-102995800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:102989200-103002400	Weak transcription	Esophagus	oesophagus
7	chr7:102989200-103006200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:102989200-103007800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:102989200-103010600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:102989200-103011400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr7:102989200-103013200	Weak transcription	Stomach Mucosa	stomach
12	chr7:102989600-102994800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr7:102989600-103000800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr7:102989600-103002400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr7:102989600-103002600	Weak transcription	Ovary	ovary
16	chr7:102989600-103007000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr7:102989800-103021200	Weak transcription	Fetal Heart	heart
18	chr7:102990000-102993200	Weak transcription	HSMM	muscle
19	chr7:102990000-103000800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr7:102990200-102994800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:102990200-102995000	Weak transcription	Colonic Mucosa	Colon
22	chr7:102990200-102995000	Weak transcription	Fetal Lung	lung
23	chr7:102990200-102995200	Weak transcription	Fetal Brain Male	brain
24	chr7:102990200-102995800	Weak transcription	Pancreas	Pancrea
25	chr7:102990200-102996000	Weak transcription	HSMMtube	muscle
26	chr7:102990200-103002400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr7:102990400-102993600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr7:102990400-102993800	Genic enhancers	Liver	Liver
29	chr7:102990400-102995200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr7:102990600-102993200	Weak transcription	HUVEC	blood vessel
31	chr7:102990600-102996000	Weak transcription	Brain Substantia Nigra	brain
32	chr7:102990600-102996400	Weak transcription	Fetal Kidney	kidney
33	chr7:102990600-102998800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr7:102990600-103010600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:102990800-102994600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr7:102990800-102995400	Weak transcription	Brain Anterior Caudate	brain
37	chr7:102990800-102997800	Weak transcription	Brain Germinal Matrix	brain
38	chr7:102990800-103011200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr7:102991000-102994000	Strong transcription	Thymus	Thymus
40	chr7:102991000-103010800	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr7:102991000-103011400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr7:102991200-102998800	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr7:102991200-103010200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr7:102991400-102993400	Strong transcription	Primary T cells from cord blood	blood
45	chr7:102991400-102995200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr7:102991400-102996600	Strong transcription	Fetal Muscle Trunk	muscle
47	chr7:102991400-103002400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr7:102991400-103009000	Strong transcription	A549	lung
49	chr7:102991400-103009400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr7:102991400-103011200	Strong transcription	Primary monocytes fromperipheralblood	blood

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