Variant report

Variant	rs12192828
Chromosome Location	chr6:30792492-30792493
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30788846..30792943-chr6:30842643..30845954,4	K562	blood:
2	chr6:30787789..30791714-chr6:30792255..30797305,10	K562	blood:
3	chr6:30790580..30792943-chr6:30844011..30845954,2	K562	blood:
4	chr6:30790825..30794312-chr6:30874168..30877841,3	MCF-7	breast:
5	chr6:30787837..30792214-chr6:30792255..30797817,7	K562	blood:
6	chr6:30790785..30794407-chr6:30878846..30882316,4	MCF-7	breast:
7	chr6:30703666..30722133-chr6:30776009..30801352,184	MCF-7	breast:
8	chr6:30780781..30784942-chr6:30792103..30795715,5	K562	blood:
9	chr6:30780598..30803497-chr6:30842531..30855110,80	MCF-7	breast:
10	chr6:30792427..30796566-chr6:30845190..30846951,4	MCF-7	breast:
11	chr6:30703055..30723531-chr6:30783853..30800217,151	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000264731	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000213780	Chromatin interaction
ENSG00000237775	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000263608	Chromatin interaction
ENSG00000201988	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10807071	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12189560	0.84[EUR][1000 genomes]
rs12189986	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12190167	0.89[EUR][1000 genomes]
rs12190453	0.85[EUR][1000 genomes]
rs12192177	0.83[EUR][1000 genomes]
rs12192178	0.83[EUR][1000 genomes]
rs12192205	0.85[EUR][1000 genomes]
rs12192430	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192704	0.85[EUR][1000 genomes]
rs12192760	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195469	0.85[EUR][1000 genomes]
rs12195508	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195605	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12195964	0.85[EUR][1000 genomes]
rs12197154	0.88[EUR][1000 genomes]
rs12197221	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198723	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198842	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12199559	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12199612	0.81[EUR][1000 genomes]
rs12200562	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12200829	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12202570	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12202778	0.82[EUR][1000 genomes]
rs12202957	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12203011	0.84[EUR][1000 genomes]
rs12203199	0.84[EUR][1000 genomes]
rs12203797	0.85[EUR][1000 genomes]
rs12204146	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12204167	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12205844	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205961	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206022	0.85[EUR][1000 genomes]
rs12206742	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12206930	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12207652	0.82[EUR][1000 genomes]
rs12208098	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12208771	0.84[EUR][1000 genomes]
rs12209725	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12210111	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12210318	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12210590	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12212837	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213493	0.85[EUR][1000 genomes]
rs12213497	0.85[EUR][1000 genomes]
rs12214232	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12214398	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12215119	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264372	0.82[ASN][1000 genomes]
rs16897921	0.85[EUR][1000 genomes]
rs16897932	0.85[EUR][1000 genomes]
rs17189483	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17189490	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17195830	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17195837	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394414	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28744161	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28744171	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28766294	0.87[EUR][1000 genomes]
rs28877339	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28890780	0.82[EUR][1000 genomes]
rs4248152	0.85[EUR][1000 genomes]
rs4327730	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4409219	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4711240	0.84[EUR][1000 genomes]
rs4711241	0.85[EUR][1000 genomes]
rs4713373	0.84[EUR][1000 genomes]
rs4713376	0.84[EUR][1000 genomes]
rs4713386	0.85[EUR][1000 genomes]
rs4713387	0.84[EUR][1000 genomes]
rs4713388	0.85[EUR][1000 genomes]
rs4713391	0.85[EUR][1000 genomes]
rs59293911	0.84[EUR][1000 genomes]
rs62400964	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400965	0.80[EUR][1000 genomes]
rs62400966	0.80[EUR][1000 genomes]
rs62400977	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400978	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400979	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62400980	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400981	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62408707	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62408708	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62408709	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62408712	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62408713	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62408715	0.84[EUR][1000 genomes]
rs62408716	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62408723	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62408724	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62408725	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62408726	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62408727	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62408728	0.85[EUR][1000 genomes]
rs9501488	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
8	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12192828	PRSS16	cis	cerebellum	SCAN
rs12192828	PACSIN1	cis	cerebellum	SCAN
rs12192828	IER3	cis	lymphoblastoid	seeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30779000-30794800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:30779000-30795800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:30782000-30796000	Weak transcription	Pancreas	Pancrea
4	chr6:30782000-30797000	Weak transcription	Gastric	stomach
5	chr6:30782800-30794600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:30783400-30794600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:30786400-30792800	Enhancers	Stomach Mucosa	stomach
8	chr6:30788200-30794800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:30788200-30794800	Weak transcription	Esophagus	oesophagus
10	chr6:30788400-30795800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:30788400-30796000	Weak transcription	Lung	lung
12	chr6:30788600-30794800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:30788600-30794800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:30788600-30795800	Weak transcription	Left Ventricle	heart
15	chr6:30788600-30795800	Weak transcription	Right Ventricle	heart
16	chr6:30788800-30795800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:30789200-30792800	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr6:30789400-30793000	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr6:30790200-30795800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:30790200-30795800	Weak transcription	Fetal Intestine Small	intestine
21	chr6:30790200-30796200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:30790400-30792600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr6:30790400-30793200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:30790400-30794400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr6:30790400-30794400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr6:30790400-30794600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr6:30790400-30794600	Weak transcription	HSMM	muscle
28	chr6:30790400-30794600	Weak transcription	HUVEC	blood vessel
29	chr6:30790400-30794800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:30790400-30794800	Weak transcription	Dnd41	blood
31	chr6:30790400-30795000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:30790400-30795600	Weak transcription	Liver	Liver
33	chr6:30790400-30795800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr6:30790400-30795800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:30790400-30795800	Weak transcription	Aorta	Aorta
36	chr6:30790400-30795800	Weak transcription	Brain Angular Gyrus	brain
37	chr6:30790400-30795800	Weak transcription	Brain Anterior Caudate	brain
38	chr6:30790400-30795800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr6:30790400-30795800	Weak transcription	Fetal Kidney	kidney
40	chr6:30790600-30794200	Weak transcription	K562	blood
41	chr6:30790600-30794600	Weak transcription	NH-A	brain
42	chr6:30790600-30794800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:30790600-30795800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:30790600-30796000	Weak transcription	Fetal Lung	lung
45	chr6:30790800-30792800	Enhancers	A549	lung
46	chr6:30790800-30792800	Enhancers	HepG2	liver
47	chr6:30790800-30793600	Weak transcription	Hela-S3	cervix
48	chr6:30790800-30794400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr6:30790800-30794400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr6:30790800-30794600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links