Variant report

Variant	rs798530
Chromosome Location	chr7:2772261-2772262
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:2760677..2762584-chr7:2771267..2773265,2	MCF-7	breast:
2	chr7:2756029..2757761-chr7:2771814..2773662,2	MCF-7	breast:
3	chr7:2768256..2774537-chr7:2775031..2780281,7	K562	blood:
4	chr7:2726497..2731953-chr7:2769904..2775258,10	MCF-7	breast:
5	chr7:2751778..2761552-chr7:2768388..2775125,13	K562	blood:
6	chr7:2770824..2773530-chr7:2796217..2798133,2	K562	blood:
7	chr7:2770258..2772875-chr7:2776418..2779322,2	MCF-7	breast:
8	chr7:2769685..2774579-chr7:2777594..2780364,4	K562	blood:
9	chr7:2772073..2775942-chr7:2781505..2783799,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000174945	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1182206	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs208345	0.82[CHB][hapmap]
rs208346	0.91[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs208354	0.90[CHB][hapmap]
rs208356	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs2251718	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2255541	0.86[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2255782	0.91[CHB][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2258709	0.83[CHB][hapmap]
rs2258960	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2266923	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2266925	0.86[CHB][hapmap]
rs2527682	0.85[EUR][1000 genomes]
rs2527686	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs2527689	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2533886	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs2533888	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs2644272	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs2644276	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2644306	0.83[CHB][hapmap]
rs2644311	0.92[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes]
rs2693566	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3846992	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs709280	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs709281	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs757786	0.82[CHB][hapmap]
rs757789	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs757790	0.82[ASN][1000 genomes]
rs7790322	0.83[CHB][hapmap]
rs798501	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798504	0.84[EUR][1000 genomes]
rs798505	0.82[EUR][1000 genomes]
rs798509	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798515	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs798516	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs798517	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs798519	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798520	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798521	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798522	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798523	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798524	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798525	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798527	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs798529	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798532	0.86[CHB][hapmap]
rs798549	0.81[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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv605872	chr7:2770899-2776698	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs798530	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs798530	GNA12	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2752400-2796000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:2754800-2774200	Weak transcription	Fetal Brain Male	brain
3	chr7:2756000-2777800	Weak transcription	Psoas Muscle	Psoas
4	chr7:2757600-2772800	Weak transcription	Small Intestine	intestine
5	chr7:2759200-2774000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr7:2761000-2773000	Weak transcription	A549	lung
7	chr7:2761000-2774200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr7:2761000-2774200	Weak transcription	GM12878-XiMat	blood
9	chr7:2761000-2774800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr7:2761000-2796200	Weak transcription	Hela-S3	cervix
11	chr7:2761000-2797000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr7:2761400-2772800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:2762600-2772800	Strong transcription	Fetal Intestine Large	intestine
14	chr7:2764600-2774400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:2764800-2772600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr7:2766600-2773400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr7:2767200-2773000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:2767800-2773000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr7:2768000-2772600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:2768400-2773000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:2768400-2773400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:2768400-2773600	Strong transcription	HepG2	liver
23	chr7:2768400-2776600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr7:2768600-2772800	Weak transcription	Stomach Mucosa	stomach
25	chr7:2768600-2773600	Strong transcription	Primary T cells from cord blood	blood
26	chr7:2768800-2772600	Weak transcription	Fetal Heart	heart
27	chr7:2768800-2773200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr7:2769000-2772400	Strong transcription	Osteobl	bone
29	chr7:2769000-2772800	Weak transcription	NH-A	brain
30	chr7:2769000-2773200	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr7:2769600-2772800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr7:2769600-2772800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr7:2769800-2772400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr7:2770000-2773200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr7:2770200-2773000	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr7:2770200-2773000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr7:2770400-2772600	Weak transcription	Colon Smooth Muscle	Colon
38	chr7:2770400-2772800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:2770400-2772800	Weak transcription	Brain Angular Gyrus	brain
40	chr7:2770600-2775000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr7:2770800-2772800	Strong transcription	Fetal Intestine Small	intestine
42	chr7:2770800-2772800	Strong transcription	HSMM	muscle
43	chr7:2770800-2773000	Strong transcription	Fetal Stomach	stomach
44	chr7:2771000-2772600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr7:2771000-2773000	Weak transcription	Brain Substantia Nigra	brain
46	chr7:2771000-2773400	Weak transcription	Thymus	Thymus
47	chr7:2771000-2774600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr7:2771000-2780400	Weak transcription	Aorta	Aorta
49	chr7:2771200-2772400	Weak transcription	Adipose Nuclei	Adipose
50	chr7:2771200-2772400	Weak transcription	Brain Cingulate Gyrus	brain

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