Variant report

Variant	rs38409
Chromosome Location	chr7:30538651-30538652
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:30520573..30522564-chr7:30538641..30540163,2	MCF-7	breast:
2	chr7:30537997..30542227-chr7:30542503..30545909,8	MCF-7	breast:
3	chr7:30537384..30539209-chr7:30541692..30544270,2	MCF-7	breast:
4	chr7:30537020..30540018-chr7:30543361..30545288,2	K562	blood:

Variant related genes	Relation type
ENSG00000006625	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs28679	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs38406	0.90[ASN][1000 genomes]
rs38407	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs38408	0.93[ASN][1000 genomes]
rs38410	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs38411	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs38413	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs38414	0.86[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs38415	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs38416	0.86[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs38417	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs38418	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs38419	0.95[ASN][1000 genomes]
rs38420	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs38421	0.92[ASN][1000 genomes]
rs38422	0.95[ASN][1000 genomes]
rs38423	0.94[ASN][1000 genomes]
rs38425	0.94[ASN][1000 genomes]
rs38426	0.94[ASN][1000 genomes]
rs38427	0.95[ASN][1000 genomes]
rs38428	0.84[ASN][1000 genomes]
rs38429	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs38430	0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs38432	0.94[ASN][1000 genomes]
rs38433	0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs38434	0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs38435	0.83[ASN][1000 genomes]
rs38436	0.83[ASN][1000 genomes]
rs38437	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs38438	0.92[ASN][1000 genomes]
rs38440	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs38441	0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs38442	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs38444	0.84[ASN][1000 genomes]
rs38445	0.85[ASN][1000 genomes]
rs38446	0.85[ASN][1000 genomes]
rs38447	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs38448	0.86[ASN][1000 genomes]
rs38450	0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs38451	0.84[ASN][1000 genomes]
rs38452	0.86[ASN][1000 genomes]
rs38453	0.83[ASN][1000 genomes]
rs38454	0.83[ASN][1000 genomes]
rs38455	0.81[ASN][1000 genomes]
rs38456	0.85[ASN][1000 genomes]
rs38458	0.85[ASN][1000 genomes]
rs38460	0.83[ASN][1000 genomes]
rs38461	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs38462	0.85[ASN][1000 genomes]
rs38463	0.83[ASN][1000 genomes]
rs38464	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs38465	0.82[ASN][1000 genomes]
rs38466	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs38467	0.84[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs38468	0.84[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs38469	0.84[CEU][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs38471	0.84[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs38473	0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs38474	0.88[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap]
rs38478	0.91[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap]
rs38480	0.82[CEU][hapmap]
rs39738	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs40237	0.94[ASN][1000 genomes]
rs4258	0.81[CEU][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4259	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4260	0.86[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs973002	0.81[CHB][hapmap]

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs38409	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs38409	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs38409	AC005154.8	cis	Whole Blood	GTEx
rs38409	AC005154.6	cis	lung	GTEx
rs38409	PRR15	cis	cerebellum	SCAN
rs38409	AC005154.6	cis	Nerve Tibial	GTEx
rs38409	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs38409	C7orf41	cis	cerebellum	SCAN
rs38409	AC005154.6	cis	Muscle Skeletal	GTEx
rs38409	AC005154.6	cis	Esophagus Muscularis	GTEx
rs38409	AC005154.6	cis	Artery Tibial	GTEx
rs38409	AC005154.6	cis	Stomach	GTEx
rs38409	CRHR2	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30519200-30542400	Weak transcription	Spleen	Spleen
2	chr7:30519200-30542600	Weak transcription	Fetal Kidney	kidney
3	chr7:30519200-30542800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:30528000-30541600	Weak transcription	Fetal Heart	heart
5	chr7:30529800-30542400	Weak transcription	NHLF	lung
6	chr7:30530400-30542600	Weak transcription	Esophagus	oesophagus
7	chr7:30532000-30543000	Weak transcription	Brain Anterior Caudate	brain
8	chr7:30532400-30541400	Weak transcription	Psoas Muscle	Psoas
9	chr7:30532400-30542400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr7:30532800-30542600	Weak transcription	Brain Angular Gyrus	brain
11	chr7:30532800-30542600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:30532800-30542800	Weak transcription	Colon Smooth Muscle	Colon
13	chr7:30533000-30543600	Weak transcription	Aorta	Aorta
14	chr7:30533200-30541600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr7:30533200-30542400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr7:30533200-30542600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr7:30533200-30542800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr7:30533200-30542800	Weak transcription	Small Intestine	intestine
19	chr7:30533200-30543000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr7:30533400-30540200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:30533400-30541400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr7:30533400-30542000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr7:30533600-30542400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr7:30533600-30542800	Weak transcription	Fetal Lung	lung
25	chr7:30533800-30541200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr7:30533800-30542400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr7:30533800-30542600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr7:30533800-30542600	Weak transcription	Right Ventricle	heart
29	chr7:30534000-30539000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:30534000-30542000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr7:30534200-30539400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr7:30534200-30540200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:30534200-30542800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr7:30534200-30543000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr7:30534400-30541400	Weak transcription	Hela-S3	cervix
36	chr7:30534400-30542600	Weak transcription	Brain Hippocampus Middle	brain
37	chr7:30534400-30542600	Weak transcription	Pancreas	Pancrea
38	chr7:30534400-30542800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr7:30534400-30542800	Weak transcription	Fetal Muscle Leg	muscle
40	chr7:30534600-30539400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr7:30534600-30542600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr7:30534800-30538800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr7:30534800-30539000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr7:30534800-30542400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr7:30534800-30542800	Weak transcription	Fetal Brain Male	brain
46	chr7:30534800-30542800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr7:30534800-30543000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:30534800-30543000	Weak transcription	Brain Substantia Nigra	brain
49	chr7:30534800-30543200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr7:30535000-30539000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links