Variant report

Variant	rs6972398
Chromosome Location	chr7:127548231-127548232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127540563..127543536-chr7:127545716..127548575,3	K562	blood:
2	chr7:127545052..127549084-chr7:127551154..127554840,4	K562	blood:
3	chr7:127539496..127544017-chr7:127546415..127549727,4	MCF-7	breast:
4	chr7:127547698..127550637-chr7:127555388..127557682,2	K562	blood:
5	chr7:127545052..127549084-chr7:127550970..127554840,5	K562	blood:
6	chr7:127532785..127535479-chr7:127547850..127550126,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1019578	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10228031	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1025075	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10487503	0.84[ASN][1000 genomes]
rs1073155	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1440973	0.94[ASN][1000 genomes]
rs1468701	0.90[ASN][1000 genomes]
rs1468702	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs17133046	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs17151515	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17151567	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17151575	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17151650	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1833146	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1966517	0.89[ASN][1000 genomes]
rs2402873	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs325438	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs325439	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs325443	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs325448	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs325449	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs325450	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4728078	0.94[ASN][1000 genomes]
rs4728082	0.84[ASN][1000 genomes]
rs4731379	0.94[ASN][1000 genomes]
rs4731382	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4731383	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4731384	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs61743021	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6467142	0.94[ASN][1000 genomes]
rs6467146	0.94[ASN][1000 genomes]
rs6467147	0.94[ASN][1000 genomes]
rs6467149	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6467150	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6467151	0.94[ASN][1000 genomes]
rs6467154	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6946590	0.84[ASN][1000 genomes]
rs6950211	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6952123	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6952734	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6953530	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6964714	1.00[ASN][1000 genomes]
rs6972816	0.84[ASN][1000 genomes]
rs6975274	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6976145	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6979918	0.94[ASN][1000 genomes]
rs698409	0.94[ASN][1000 genomes]
rs712720	0.94[ASN][1000 genomes]
rs73721253	0.89[ASN][1000 genomes]
rs73721258	0.89[ASN][1000 genomes]
rs73721264	0.89[ASN][1000 genomes]
rs7458839	0.84[ASN][1000 genomes]
rs7791000	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7794303	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7794328	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7809182	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv526535	chr7:127445594-127623840	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1024743	chr7:127498695-127670004	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127528800-127569200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr7:127529000-127557200	Weak transcription	Esophagus	oesophagus
3	chr7:127529200-127548400	Weak transcription	Right Ventricle	heart
4	chr7:127529200-127569400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr7:127529400-127551000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:127532200-127569200	Weak transcription	Hela-S3	cervix
7	chr7:127532400-127569200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr7:127539000-127556400	Weak transcription	Psoas Muscle	Psoas
9	chr7:127541000-127569200	Weak transcription	Fetal Muscle Leg	muscle
10	chr7:127541200-127569400	Weak transcription	Left Ventricle	heart
11	chr7:127541400-127550800	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr7:127542600-127553000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr7:127542600-127553000	Weak transcription	Ovary	ovary
14	chr7:127542600-127553400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr7:127542800-127552800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr7:127542800-127554200	Weak transcription	Gastric	stomach
17	chr7:127543400-127549200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr7:127543600-127551400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr7:127544000-127548400	Genic enhancers	GM12878-XiMat	blood
20	chr7:127544000-127549000	Enhancers	HepG2	liver
21	chr7:127544000-127549600	Enhancers	Fetal Intestine Small	intestine
22	chr7:127544200-127551000	Weak transcription	Spleen	Spleen
23	chr7:127544600-127551400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr7:127544800-127551000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr7:127544800-127554400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:127544800-127560600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr7:127545000-127549400	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr7:127545000-127550800	Weak transcription	Fetal Brain Male	brain
29	chr7:127545000-127569200	Weak transcription	Thymus	Thymus
30	chr7:127545000-127569200	Weak transcription	HSMMtube	muscle
31	chr7:127545200-127550800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr7:127545200-127552400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr7:127545600-127552400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr7:127545800-127550000	Enhancers	Fetal Intestine Large	intestine
35	chr7:127545800-127552800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr7:127545800-127555000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr7:127545800-127569200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr7:127546000-127548600	Enhancers	Small Intestine	intestine
39	chr7:127546000-127549000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr7:127546000-127550800	Weak transcription	Right Atrium	heart
41	chr7:127546000-127566800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr7:127546200-127549000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr7:127546200-127550600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:127546200-127552800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr7:127546200-127553200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr7:127546200-127554200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr7:127546200-127559000	Weak transcription	HSMM	muscle
48	chr7:127546200-127560400	Weak transcription	Pancreas	Pancrea
49	chr7:127546200-127569200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr7:127546400-127548400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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