Variant report

Variant	rs1999386
Chromosome Location	chr9:96289743-96289744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96289697..96291647-chr9:96299616..96302310,2	K562	blood:
2	chr9:96283749..96287240-chr9:96288399..96291092,3	K562	blood:
3	chr9:96212405..96217053-chr9:96287727..96291116,5	MCF-7	breast:
4	chr9:96287109..96291346-chr9:96292892..96295512,4	MCF-7	breast:
5	chr9:96289339..96291734-chr9:96339194..96341014,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188938	Chromatin interaction
ENSG00000048828	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

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]
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[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][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]
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]
rs3893381	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]
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[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1999386	SHC3	cis	cerebellum	SCAN
rs1999386	FANCC	cis	parietal	SCAN
rs1999386	RP11-165J3.6	cis	Thyroid	GTEx
rs1999386	FAM120AOS	cis	cerebellum	SCAN
rs1999386	RP11-165J3.6	cis	Esophagus Muscularis	GTEx
rs1999386	RP11-165J3.6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96260800-96290800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:96263200-96290200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:96270800-96291600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr9:96274000-96291000	Weak transcription	Small Intestine	intestine
5	chr9:96275800-96299600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr9:96276000-96295600	Weak transcription	Stomach Mucosa	stomach
7	chr9:96276000-96300000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr9:96276200-96290200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr9:96276200-96291400	Weak transcription	Brain Germinal Matrix	brain
10	chr9:96278400-96310800	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr9:96278400-96327000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr9:96278400-96327200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr9:96278400-96328200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr9:96278600-96311200	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr9:96278800-96298600	Strong transcription	Placenta	Placenta
16	chr9:96279000-96297400	Strong transcription	HepG2	liver
17	chr9:96279000-96298600	Strong transcription	GM12878-XiMat	blood
18	chr9:96279000-96310400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr9:96279000-96327400	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr9:96281400-96295600	Weak transcription	Psoas Muscle	Psoas
21	chr9:96282200-96323400	Strong transcription	Primary B cells from cord blood	blood
22	chr9:96283000-96297200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr9:96283200-96291200	Weak transcription	Fetal Brain Female	brain
24	chr9:96283600-96297400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr9:96284200-96290600	Enhancers	Fetal Heart	heart
26	chr9:96284400-96297800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:96284600-96327200	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr9:96284600-96328200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:96284800-96292000	Strong transcription	Fetal Intestine Small	intestine
30	chr9:96284800-96297400	Strong transcription	Fetal Stomach	stomach
31	chr9:96284800-96309800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr9:96284800-96327200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:96285000-96292000	Strong transcription	Fetal Muscle Leg	muscle
34	chr9:96285000-96292200	Strong transcription	Primary T cells from cord blood	blood
35	chr9:96285000-96292200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr9:96285000-96292200	Strong transcription	Fetal Muscle Trunk	muscle
37	chr9:96285000-96293200	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr9:96285000-96297200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr9:96285000-96297600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr9:96285000-96297800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr9:96285000-96298800	Strong transcription	A549	lung
42	chr9:96285000-96301400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:96285000-96304000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr9:96285000-96327000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr9:96285000-96327000	Strong transcription	Dnd41	blood
46	chr9:96285200-96291000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr9:96285200-96291800	Strong transcription	Primary hematopoietic stem cells	blood
48	chr9:96285200-96296600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr9:96285200-96299600	Strong transcription	Fetal Intestine Large	intestine
50	chr9:96285200-96299600	Strong transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links