Variant report

Variant	rs7025805
Chromosome Location	chr9:96243745-96243746
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:96234460..96236110-chr9:96243450..96245599,2	MCF-7	breast:
2	chr9:96220347..96222637-chr9:96242128..96243998,2	MCF-7	breast:
3	chr9:96240211..96242392-chr9:96243662..96246042,2	MCF-7	breast:
4	chr9:96232297..96234859-chr9:96241804..96243993,2	MCF-7	breast:
5	chr9:96241899..96244084-chr9:96246554..96249492,2	MCF-7	breast:
6	chr9:96211777..96216293-chr9:96240145..96244458,5	MCF-7	breast:
7	chr9:96239024..96243784-chr9:96244555..96247463,4	K562	blood:
8	chr9:96239024..96241783-chr9:96243346..96246055,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000188938	Chromatin interaction
ENSG00000048828	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10429558	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10512224	0.82[YRI][hapmap]
rs11975	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12341488	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12554020	0.81[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1331588	0.95[LWK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs3815563	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3897285	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs4552973	0.81[CEU][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55702483	0.80[AFR][1000 genomes]
rs55812345	0.96[AFR][1000 genomes]
rs59326991	0.95[AFR][1000 genomes]
rs59483310	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59582399	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60076242	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60212988	0.84[AFR][1000 genomes]
rs6479482	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6479483	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479487	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6479494	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6479495	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7020459	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7023933	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7028729	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7035657	0.87[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7036984	0.87[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7038564	0.89[LWK][hapmap]
rs7048853	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7850322	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7853605	0.81[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes]
rs7857183	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7859267	0.84[CHB][hapmap]
rs7860098	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7861929	0.96[AFR][1000 genomes]
rs7862998	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7870210	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7874126	0.96[YRI][hapmap];0.96[AFR][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7025805	RP11-165J3.6	cis	Thyroid	GTEx
rs7025805	OGN	cis	parietal	SCAN
rs7025805	RP11-165J3.6	cis	Skin Sun Exposed Lower leg	GTEx
rs7025805	RP11-165J3.6	cis	Artery Tibial	GTEx
rs7025805	RP11-165J3.6	cis	Nerve Tibial	GTEx
rs7025805	SHC3	cis	cerebellum	SCAN
rs7025805	FAM120AOS	Cis_1M	lymphoblastoid	RTeQTL
rs7025805	RP11-165J3.6	cis	Esophagus Muscularis	GTEx
rs7025805	ANKRD19	cis	cerebellum	SCAN
rs7025805	FANCC	cis	cerebellum	SCAN

Chromatin state (count:127 , 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	chr9:96230000-96244800	Weak transcription	Thymus	Thymus
3	chr9:96231600-96244800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:96231600-96244800	Weak transcription	Aorta	Aorta
5	chr9:96231600-96246400	Weak transcription	Brain Germinal Matrix	brain
6	chr9:96231600-96246400	Weak transcription	Spleen	Spleen
7	chr9:96231600-96251600	Weak transcription	Pancreas	Pancrea
8	chr9:96231600-96256400	Weak transcription	NH-A	brain
9	chr9:96231800-96245000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:96231800-96246400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:96231800-96246600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr9:96232000-96246400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr9:96232600-96251800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr9:96232800-96262600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr9:96233400-96248000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr9:96233600-96245000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:96233600-96246400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr9:96233600-96246400	Weak transcription	Gastric	stomach
19	chr9:96233600-96248600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr9:96233800-96244800	Weak transcription	Brain Hippocampus Middle	brain
21	chr9:96233800-96245000	Weak transcription	Brain Substantia Nigra	brain
22	chr9:96233800-96258400	Weak transcription	Colonic Mucosa	Colon
23	chr9:96233800-96258600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr9:96234000-96250000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:96234000-96254000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr9:96234400-96259400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr9:96235800-96253600	Weak transcription	Stomach Mucosa	stomach
28	chr9:96236000-96246400	Weak transcription	Ovary	ovary
29	chr9:96238200-96248600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr9:96238400-96246000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr9:96238400-96246400	Weak transcription	NHLF	lung
32	chr9:96238400-96252800	Strong transcription	Placenta	Placenta
33	chr9:96238400-96258400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:96238800-96246400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr9:96238800-96246400	Weak transcription	HSMM	muscle
36	chr9:96238800-96256400	Weak transcription	Fetal Kidney	kidney
37	chr9:96239400-96246400	Weak transcription	Brain Anterior Caudate	brain
38	chr9:96239400-96251800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr9:96239600-96263200	Weak transcription	Small Intestine	intestine
40	chr9:96240000-96244000	Weak transcription	Fetal Muscle Leg	muscle
41	chr9:96240000-96245800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr9:96240000-96246200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:96240000-96249800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:96240200-96244800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr9:96240200-96255800	Weak transcription	Fetal Brain Female	brain
46	chr9:96240800-96245400	Strong transcription	Fetal Intestine Small	intestine
47	chr9:96241200-96244800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr9:96241200-96246000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:96241200-96246400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr9:96241600-96262400	Strong transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links