Variant report

Variant	rs6974877
Chromosome Location	chr7:138172525-138172526
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10155993	0.92[ASN][1000 genomes]
rs10215281	0.92[ASN][1000 genomes]
rs10227693	0.83[ASN][1000 genomes]
rs10232771	0.89[ASN][1000 genomes]
rs10247380	0.83[ASN][1000 genomes]
rs10248731	0.82[ASN][1000 genomes]
rs10258706	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1030961	0.88[ASN][1000 genomes]
rs1077772	0.89[ASN][1000 genomes]
rs1116324	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11976614	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12112459	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12666310	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1421604	0.92[ASN][1000 genomes]
rs1544733	0.84[ASN][1000 genomes]
rs1659830	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1659832	0.80[AMR][1000 genomes]
rs1673203	0.84[ASN][1000 genomes]
rs1673204	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1673206	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1673207	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17364560	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17461551	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2353354	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2353355	0.81[ASN][1000 genomes]
rs3757381	0.89[ASN][1000 genomes]
rs3778705	0.86[ASN][1000 genomes]
rs3807155	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3807156	0.91[ASN][1000 genomes]
rs3807157	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55723768	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56092804	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57407834	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58562866	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62485261	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62485263	0.88[ASN][1000 genomes]
rs62485264	0.87[ASN][1000 genomes]
rs62487613	0.87[ASN][1000 genomes]
rs62487615	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62487616	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62487619	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6467776	0.93[ASN][1000 genomes]
rs6467778	0.92[ASN][1000 genomes]
rs6467780	0.88[ASN][1000 genomes]
rs6467782	0.81[ASN][1000 genomes]
rs6467783	0.81[ASN][1000 genomes]
rs6948094	0.81[ASN][1000 genomes]
rs6954285	0.81[ASN][1000 genomes]
rs6959574	0.83[ASN][1000 genomes]
rs6963539	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6970175	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6978524	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs728092	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs749546	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7795981	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7808392	0.91[ASN][1000 genomes]
rs888609	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9791462	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs985299	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34048	chr7:137724092-138213119	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831153	chr7:138078179-138265648	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1030956	chr7:138163169-138579519	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv981589	chr7:138163846-138177455	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:138147200-138183800	Weak transcription	Primary B cells from cord blood	blood
2	chr7:138147200-138189000	Weak transcription	Thymus	Thymus
3	chr7:138149800-138188600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:138153800-138184200	Weak transcription	Fetal Stomach	stomach
5	chr7:138155200-138184200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:138157600-138191400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr7:138160200-138175000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr7:138160600-138182200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr7:138161800-138195800	Weak transcription	Fetal Brain Female	brain
10	chr7:138162000-138175200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr7:138163600-138183400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr7:138163600-138184000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr7:138163600-138184200	Weak transcription	Aorta	Aorta
14	chr7:138163600-138184200	Weak transcription	Fetal Thymus	thymus
15	chr7:138163800-138175400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr7:138164000-138191400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr7:138164000-138199800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:138164200-138173400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr7:138164400-138175400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:138164400-138175400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr7:138164400-138176800	Weak transcription	Pancreas	Pancrea
22	chr7:138164400-138184200	Weak transcription	Ovary	ovary
23	chr7:138165000-138192000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr7:138165600-138175600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr7:138165600-138184000	Weak transcription	Primary T cells from cord blood	blood
26	chr7:138166600-138184000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr7:138166800-138175200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr7:138166800-138175800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr7:138167000-138177800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr7:138168000-138181400	Weak transcription	Fetal Intestine Small	intestine
31	chr7:138168000-138196200	Weak transcription	Left Ventricle	heart
32	chr7:138168200-138178200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:138168600-138175800	Weak transcription	Liver	Liver
34	chr7:138168600-138176000	Weak transcription	Stomach Mucosa	stomach
35	chr7:138168800-138175200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:138168800-138175400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr7:138168800-138175800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr7:138168800-138184200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr7:138169000-138190200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr7:138169400-138173200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr7:138169400-138175800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr7:138169600-138175200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr7:138169600-138175400	Weak transcription	HepG2	liver
44	chr7:138170000-138174800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr7:138170600-138175400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr7:138170800-138175000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr7:138172000-138172600	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr7:138172400-138172800	Enhancers	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links