Variant report

Variant	rs9606830
Chromosome Location	chr22:31717799-31717800
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31709484..31711779-chr22:31717632..31720402,2	MCF-7	breast:
2	chr22:31707932..31710940-chr22:31717264..31720146,3	MCF-7	breast:
3	chr22:31686050..31689406-chr22:31717543..31719955,3	MCF-7	breast:
4	chr22:31717438..31719126-chr22:31741074..31742851,2	MCF-7	breast:
5	chr22:31717116..31718707-chr22:31727268..31729171,2	MCF-7	breast:
6	chr22:31717141..31720264-chr22:31721162..31724209,3	MCF-7	breast:
7	chr22:31716552..31720411-chr22:31737188..31740902,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100105	Chromatin interaction
ENSG00000100100	Chromatin interaction
ENSG00000228839	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1034588	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1034589	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12152166	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13054220	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13056485	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs131205	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13158	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1858821	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2040533	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2073857	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2078803	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2079431	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2106294	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2228619	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2232170	0.85[CEU][hapmap]
rs2232176	0.85[CEU][hapmap]
rs2273249	0.95[CEU][hapmap]
rs2273251	0.95[CEU][hapmap]
rs2283879	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2283881	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2413033	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2413034	0.81[EUR][1000 genomes]
rs2413035	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2413046	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2413047	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2413049	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2899164	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs34545960	0.84[EUR][1000 genomes]
rs4141404	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4299418	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4603880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820042	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820043	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4820951	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820955	1.00[CEU][hapmap]
rs4820962	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4820963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749224	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs5749229	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5749243	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5749265	0.85[EUR][1000 genomes]
rs5749267	0.84[EUR][1000 genomes]
rs5749268	0.84[EUR][1000 genomes]
rs5749270	0.84[EUR][1000 genomes]
rs5753521	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753543	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753597	0.85[EUR][1000 genomes]
rs5753601	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs5753609	0.90[CEU][hapmap]
rs5753610	0.84[EUR][1000 genomes]
rs5753612	0.83[EUR][1000 genomes]
rs5753613	0.83[EUR][1000 genomes]
rs5753632	0.95[CEU][hapmap]
rs5753639	0.95[CEU][hapmap]
rs5994394	0.83[EUR][1000 genomes]
rs5997902	0.82[EUR][1000 genomes]
rs5997912	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5997913	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs5997933	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997939	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997949	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71324184	0.92[EUR][1000 genomes]
rs714909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs715510	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7285619	0.95[CEU][hapmap]
rs7287267	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7293171	0.83[EUR][1000 genomes]
rs737684	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs737887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737888	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs738657	0.95[CEU][hapmap]
rs8135344	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8135347	0.82[EUR][1000 genomes]
rs8138596	0.91[EUR][1000 genomes]
rs8141150	0.84[EUR][1000 genomes]
rs9606831	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606839	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs9606843	0.95[CEU][hapmap]
rs9609254	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609257	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9609264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609265	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609266	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609267	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9609268	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9609276	0.83[EUR][1000 genomes]
rs9609277	0.84[EUR][1000 genomes]
rs9621235	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058844	chr22:31597104-31725296	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	esv3333136	chr22:31704947-31758417	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9606830	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs9606830	SFI1	cis	Thyroid	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31693800-31720000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr22:31704800-31720200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr22:31706200-31721000	Weak transcription	HSMMtube	muscle
4	chr22:31708800-31721400	Weak transcription	Ovary	ovary
5	chr22:31709600-31718600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr22:31709600-31721200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr22:31709600-31721200	Weak transcription	HSMM	muscle
8	chr22:31709600-31721800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr22:31709800-31718200	Weak transcription	Fetal Stomach	stomach
10	chr22:31709800-31719000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr22:31709800-31720000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr22:31709800-31720800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr22:31709800-31721200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr22:31709800-31721200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr22:31709800-31721200	Weak transcription	Colonic Mucosa	Colon
16	chr22:31709800-31721200	Weak transcription	Colon Smooth Muscle	Colon
17	chr22:31709800-31722200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr22:31709800-31725400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr22:31710000-31718800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr22:31710000-31718800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr22:31710000-31719000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr22:31710000-31719800	Weak transcription	Fetal Lung	lung
23	chr22:31710000-31720000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr22:31710000-31720000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr22:31710000-31720400	Weak transcription	Placenta	Placenta
26	chr22:31710000-31720800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr22:31710000-31721000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr22:31710000-31721200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr22:31710000-31721200	Weak transcription	Fetal Kidney	kidney
30	chr22:31710000-31721200	Weak transcription	Left Ventricle	heart
31	chr22:31710000-31721200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr22:31710000-31722000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr22:31710000-31722200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr22:31710000-31722600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr22:31710000-31722600	Weak transcription	Stomach Mucosa	stomach
36	chr22:31710000-31723000	Weak transcription	NHEK	skin
37	chr22:31710000-31724000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr22:31710000-31737000	Weak transcription	Fetal Heart	heart
39	chr22:31711600-31719800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr22:31711800-31718000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr22:31712000-31718000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr22:31712000-31718200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr22:31712000-31718200	Weak transcription	Fetal Muscle Leg	muscle
44	chr22:31712000-31721000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr22:31712400-31720800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr22:31713600-31718800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr22:31714400-31718000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr22:31714400-31720400	Weak transcription	Liver	Liver
49	chr22:31714600-31720000	Weak transcription	Adipose Nuclei	Adipose
50	chr22:31714600-31721400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links