Variant report

Variant	rs6969177
Chromosome Location	chr7:7908235-7908236
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10231029	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17562330	0.87[ASN][1000 genomes]
rs2159830	0.86[ASN][1000 genomes]
rs2348767	0.87[ASN][1000 genomes]
rs6463739	0.90[ASN][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	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv887478	chr7:7670718-7917360	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv887480	chr7:7681131-7917360	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv887485	chr7:7692483-7917360	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv887489	chr7:7770203-7913311	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1027770	chr7:7797431-7957507	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv538722	chr7:7797431-7957507	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv887490	chr7:7801684-7908970	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv523479	chr7:7821594-7909899	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
13	nsv1030180	chr7:7860424-8059221	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
14	nsv1027123	chr7:7870047-7926288	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	esv1793003	chr7:7902171-7911371	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6969177	TNRC18	cis	parietal	SCAN
rs6969177	KDELR2	cis	cerebellum	SCAN
rs6969177	C1GALT1	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7895400-7908800	Weak transcription	Left Ventricle	heart
2	chr7:7895400-7918000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:7897200-7909000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:7897200-7923200	Weak transcription	Psoas Muscle	Psoas
5	chr7:7897200-7942400	Weak transcription	Aorta	Aorta
6	chr7:7901200-7915600	Weak transcription	Gastric	stomach
7	chr7:7906600-7908600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr7:7906600-7909000	Enhancers	Brain Substantia Nigra	brain
9	chr7:7906800-7909400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr7:7907000-7910400	Enhancers	Thymus	Thymus
11	chr7:7907200-7908400	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr7:7907200-7909000	Enhancers	Primary B cells from peripheral blood	blood
13	chr7:7907200-7909000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:7907200-7909000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr7:7907200-7909000	Enhancers	Fetal Thymus	thymus
16	chr7:7907200-7911400	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr7:7907400-7908400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:7907400-7908600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr7:7907400-7908600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr7:7907400-7908600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr7:7907400-7909600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr7:7907400-7909600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:7907400-7911200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr7:7907400-7911400	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr7:7907600-7908400	Flanking Active TSS	GM12878-XiMat	blood
26	chr7:7907600-7908400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr7:7907600-7908600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr7:7907600-7908600	Enhancers	K562	blood
29	chr7:7907600-7908800	Weak transcription	Brain Hippocampus Middle	brain
30	chr7:7907600-7909000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr7:7907600-7910400	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr7:7907600-7911000	Enhancers	Fetal Heart	heart
33	chr7:7907800-7908400	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr7:7907800-7908400	Enhancers	NHEK	skin
35	chr7:7907800-7910200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr7:7907800-7910200	Weak transcription	Right Atrium	heart
37	chr7:7907800-7911200	Enhancers	Fetal Brain Male	brain
38	chr7:7907800-7915200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr7:7908000-7908400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr7:7908000-7908800	Weak transcription	Brain Anterior Caudate	brain
41	chr7:7908000-7909400	Enhancers	Primary T cells from cord blood	blood
42	chr7:7908000-7909600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr7:7908000-7910200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr7:7908000-7911600	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr7:7908000-7912000	Enhancers	Brain Germinal Matrix	brain
46	chr7:7908000-7919400	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr7:7908200-7909000	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr7:7908200-7909600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr7:7908200-7909600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr7:7908200-7918800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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