Variant report

Variant	rs3893381
Chromosome Location	chr9:96281858-96281859
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96213470..96216216-chr9:96280346..96283406,4	MCF-7	breast:
2	chr9:96219136..96220997-chr9:96281166..96283983,2	MCF-7	breast:
3	chr9:96093858..96095483-chr9:96278870..96281860,2	MCF-7	breast:
4	chr9:96281724..96284045-chr9:96336142..96339221,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188938	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000197724	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12551084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12552323	1.00[ASW][hapmap]
rs12553389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12554164	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16909150	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16909158	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16909273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17532098	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1999386	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35383254	1.00[AFR][1000 genomes]
rs35540150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4255201	0.88[CEU][hapmap]
rs55654600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025666	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56073019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56275034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7038310	0.82[CEU][hapmap]
rs883783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883785	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3893381	RP11-165J3.6	cis	Skin Sun Exposed Lower leg	GTEx
rs3893381	RP11-165J3.6	cis	Esophagus Muscularis	GTEx
rs3893381	RP11-165J3.6	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96229600-96286200	Weak transcription	Fetal Brain Male	brain
2	chr9:96243000-96288000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:96260800-96290800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:96262200-96289000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:96263200-96285800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:96263200-96287600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:96263200-96290200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:96263400-96289000	Weak transcription	Fetal Kidney	kidney
9	chr9:96264000-96286600	Weak transcription	NH-A	brain
10	chr9:96264200-96288400	Weak transcription	HSMMtube	muscle
11	chr9:96265800-96286200	Weak transcription	HUVEC	blood vessel
12	chr9:96265800-96286400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr9:96268000-96286400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr9:96268600-96282200	Weak transcription	Osteobl	bone
15	chr9:96270800-96285400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr9:96270800-96291600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr9:96271600-96282200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr9:96273800-96286600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:96274000-96291000	Weak transcription	Small Intestine	intestine
20	chr9:96275800-96299600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr9:96276000-96295600	Weak transcription	Stomach Mucosa	stomach
22	chr9:96276000-96300000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr9:96276200-96286000	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:96276200-96287800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr9:96276200-96290200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr9:96276200-96291400	Weak transcription	Brain Germinal Matrix	brain
27	chr9:96277400-96282800	Weak transcription	Right Atrium	heart
28	chr9:96277400-96284200	Weak transcription	Fetal Heart	heart
29	chr9:96278200-96283200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:96278200-96283200	Strong transcription	Thymus	Thymus
31	chr9:96278200-96283400	Strong transcription	Fetal Muscle Leg	muscle
32	chr9:96278200-96283600	Strong transcription	Dnd41	blood
33	chr9:96278200-96284400	Strong transcription	Fetal Intestine Large	intestine
34	chr9:96278400-96282600	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr9:96278400-96282800	Strong transcription	Left Ventricle	heart
36	chr9:96278400-96283000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr9:96278400-96283200	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr9:96278400-96283400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr9:96278400-96283600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr9:96278400-96283800	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr9:96278400-96283800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr9:96278400-96283800	Strong transcription	Fetal Stomach	stomach
43	chr9:96278400-96284000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr9:96278400-96310800	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr9:96278400-96327000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr9:96278400-96327200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr9:96278400-96328200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr9:96278600-96283600	Strong transcription	Liver	Liver
49	chr9:96278600-96311200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr9:96278800-96283000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links