Variant report

Variant	rs11354
Chromosome Location	chr7:2768561-2768562
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2768235..2770318-chr7:2803626..2805162,2	K562	blood:
2	chr7:2768256..2774537-chr7:2775031..2780281,7	K562	blood:
3	chr7:2751778..2761552-chr7:2768388..2775125,13	K562	blood:
4	chr7:2767711..2769889-chr7:2772615..2775037,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174945	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10480003	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17339470	0.81[CHB][hapmap]
rs2266922	0.83[YRI][hapmap]
rs4719646	0.81[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs4719647	0.84[ASN][1000 genomes]
rs4719648	0.82[ASN][1000 genomes]
rs4719654	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4722006	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4722008	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6461550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6944607	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965989	0.84[ASN][1000 genomes]
rs709282	0.93[AFR][1000 genomes]
rs7797295	0.82[ASN][1000 genomes]
rs7805092	0.92[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798492	0.86[YRI][hapmap]
rs798499	1.00[YRI][hapmap]
rs798512	1.00[YRI][hapmap]
rs798531	0.93[AFR][1000 genomes]
rs9332401	0.80[CHB][hapmap]

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	nsv471227	chr7:2629020-2768864	Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1029250	chr7:2722737-2881021	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv538652	chr7:2722737-2881021	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1024023	chr7:2726210-2829581	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv538653	chr7:2726210-2829581	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1017611	chr7:2750418-2781716	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv538654	chr7:2750418-2781716	Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11354	GNA12	cis	Nerve Tibial	GTEx
rs11354	GNA12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2749400-2770600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:2749800-2770800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:2750000-2769000	Weak transcription	NHDF-Ad	bronchial
4	chr7:2752400-2796000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:2753600-2768800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:2754800-2774200	Weak transcription	Fetal Brain Male	brain
7	chr7:2755800-2770600	Weak transcription	Fetal Kidney	kidney
8	chr7:2756000-2777800	Weak transcription	Psoas Muscle	Psoas
9	chr7:2756200-2770600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr7:2757200-2770600	Weak transcription	Esophagus	oesophagus
11	chr7:2757600-2772800	Weak transcription	Small Intestine	intestine
12	chr7:2758000-2768600	Weak transcription	Right Atrium	heart
13	chr7:2758200-2769400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr7:2758600-2769400	Strong transcription	Fetal Intestine Small	intestine
15	chr7:2758600-2769800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr7:2758600-2771600	Weak transcription	K562	blood
17	chr7:2759200-2774000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr7:2759400-2771600	Strong transcription	Pancreas	Pancrea
19	chr7:2760800-2770200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr7:2761000-2768800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr7:2761000-2773000	Weak transcription	A549	lung
22	chr7:2761000-2774200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr7:2761000-2774200	Weak transcription	GM12878-XiMat	blood
24	chr7:2761000-2774800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr7:2761000-2796200	Weak transcription	Hela-S3	cervix
26	chr7:2761000-2797000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr7:2761400-2772800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr7:2761800-2769400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:2762600-2772800	Strong transcription	Fetal Intestine Large	intestine
30	chr7:2762800-2771200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr7:2762800-2771400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr7:2763600-2769400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr7:2764600-2771600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr7:2764600-2774400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr7:2764800-2771400	Strong transcription	Primary B cells from cord blood	blood
36	chr7:2764800-2772600	Strong transcription	Primary B cells from peripheral blood	blood
37	chr7:2765000-2769800	Weak transcription	Fetal Thymus	thymus
38	chr7:2765200-2771400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr7:2765800-2769200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:2766400-2769000	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr7:2766400-2769200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr7:2766400-2770200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr7:2766600-2768600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr7:2766600-2768600	Weak transcription	Primary T cells from cord blood	blood
45	chr7:2766600-2768600	Weak transcription	Brain Germinal Matrix	brain
46	chr7:2766600-2768600	Weak transcription	Brain Substantia Nigra	brain
47	chr7:2766600-2768600	Weak transcription	Right Ventricle	heart
48	chr7:2766600-2768600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr7:2766600-2768800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr7:2766600-2769000	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links