Variant report

Variant	rs9388559
Chromosome Location	chr6:127601717-127601718
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	chr6:127586756..127589878-chr6:127599119..127602914,4	MCF-7	breast:
2	chr6:127599926..127602119-chr6:127603375..127605980,3	K562	blood:
3	chr6:127597455..127599402-chr6:127601382..127603939,2	MCF-7	breast:
4	chr6:127596682..127600965-chr6:127601180..127603432,5	K562	blood:
5	chr6:127600287..127602355-chr6:127610895..127612469,2	MCF-7	breast:
6	chr6:127597627..127599604-chr6:127601180..127604567,3	K562	blood:
7	chr6:127592830..127595809-chr6:127600762..127603606,3	MCF-7	breast:
8	chr6:127586710..127590748-chr6:127601516..127606333,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000118518	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12175928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4141423	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6569484	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6569485	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6912878	0.86[AFR][1000 genomes]
rs6915597	0.86[AFR][1000 genomes]
rs6936084	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6936621	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6936813	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6938872	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6941233	0.82[ASN][1000 genomes]
rs761842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7764180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877102	0.82[JPT][hapmap]
rs9321072	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9372861	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9372862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9372863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9372865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9372866	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9375493	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9375498	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9375500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9375502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9375505	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9385420	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9388557	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9388558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388560	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9388562	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9388565	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9388570	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9398843	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9398844	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9401939	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9401945	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9401947	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9401948	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9401949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9401954	0.83[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9388559	SCGB2A2	trans	brain	seeQTL
rs9388559	SCGB1D2	trans	brain	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:127589200-127602600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:127589400-127607800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:127589600-127607800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:127589800-127603800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:127589800-127612000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:127590400-127602600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:127590400-127606400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:127590400-127607800	Weak transcription	Thymus	Thymus
9	chr6:127590600-127602000	Weak transcription	HMEC	breast
10	chr6:127590600-127602200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:127590600-127602400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:127590600-127602400	Weak transcription	Fetal Intestine Large	intestine
13	chr6:127590600-127602600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:127590600-127607800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:127590800-127601800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:127590800-127601800	Weak transcription	NH-A	brain
17	chr6:127590800-127602200	Weak transcription	HSMM	muscle
18	chr6:127590800-127602400	Weak transcription	NHLF	lung
19	chr6:127590800-127602600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:127590800-127602600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:127590800-127602600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr6:127590800-127602600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:127590800-127602600	Weak transcription	HSMMtube	muscle
24	chr6:127590800-127602600	Weak transcription	Osteobl	bone
25	chr6:127590800-127608200	Weak transcription	A549	lung
26	chr6:127591000-127602400	Weak transcription	Fetal Kidney	kidney
27	chr6:127591000-127602600	Weak transcription	Primary B cells from cord blood	blood
28	chr6:127591000-127602600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:127591000-127602800	Weak transcription	Brain Germinal Matrix	brain
30	chr6:127591000-127603000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:127591400-127602200	Weak transcription	Dnd41	blood
32	chr6:127591400-127602600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:127591400-127603000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr6:127591400-127606800	Weak transcription	Fetal Brain Male	brain
35	chr6:127591600-127601800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr6:127591600-127602000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr6:127591600-127602800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr6:127591600-127607800	Weak transcription	Fetal Heart	heart
39	chr6:127591800-127606800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr6:127592600-127602800	Weak transcription	Fetal Brain Female	brain
41	chr6:127593800-127602600	Weak transcription	Fetal Lung	lung
42	chr6:127594000-127603000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:127594200-127602400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:127594400-127606800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr6:127594600-127601800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr6:127595000-127602000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr6:127595400-127607800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr6:127596000-127602600	Weak transcription	Lung	lung
49	chr6:127596000-127607800	Weak transcription	Pancreas	Pancrea
50	chr6:127596200-127602200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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