Variant report

Variant	rs2644312
Chromosome Location	chr7:2841164-2841165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2841055..2843126-chr7:2902471..2904345,2	MCF-7	breast:
2	chr7:2598535..2600621-chr7:2839560..2841843,2	MCF-7	breast:
3	chr7:2840989..2843373-chr7:2899244..2901944,2	MCF-7	breast:
4	chr7:2838542..2841510-chr7:2843675..2845614,3	K562	blood:

Variant related genes	Relation type
ENSG00000106012	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1182172	0.85[EUR][1000 genomes]
rs1182174	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182176	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182177	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182178	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182179	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182181	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182182	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182183	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182184	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182185	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182186	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1182187	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1182188	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1182189	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1182196	0.89[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1182197	0.80[CHB][hapmap]
rs1182198	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1182199	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1182207	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1182208	0.89[CEU][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1182209	0.89[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1183085	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13243214	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1636255	0.82[CEU][hapmap]
rs1636264	0.95[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1713919	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2107964	0.91[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2158694	0.95[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2248390	0.93[ASN][1000 genomes]
rs2251491	0.93[ASN][1000 genomes]
rs2260230	0.91[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2266922	0.94[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2283779	0.89[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2283783	0.93[ASN][1000 genomes]
rs2283784	0.93[ASN][1000 genomes]
rs2527683	0.91[ASN][1000 genomes]
rs2527684	0.94[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2527687	0.94[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2527690	0.95[ASN][1000 genomes]
rs2527692	0.93[ASN][1000 genomes]
rs2527694	0.92[ASN][1000 genomes]
rs2527695	0.92[ASN][1000 genomes]
rs2527696	0.92[ASN][1000 genomes]
rs2533878	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[EUR][1000 genomes]
rs2533879	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2533882	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2533884	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2644274	0.94[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2644275	0.94[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2644294	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2644295	0.94[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2644296	0.94[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2644297	0.94[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2644298	0.92[ASN][1000 genomes]
rs35957220	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6970963	0.86[ASN][1000 genomes]
rs6978692	0.93[ASN][1000 genomes]
rs757791	0.94[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7777484	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs7807978	0.89[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs798480	0.84[ASN][1000 genomes]
rs798482	0.84[ASN][1000 genomes]
rs798485	0.91[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs798486	0.91[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs798487	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs798488	0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798489	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs798490	0.91[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798491	0.95[CEU][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs798492	0.86[JPT][hapmap]
rs798493	0.90[EUR][1000 genomes]
rs798494	0.95[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs798495	0.91[CEU][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes]
rs798496	0.81[EUR][1000 genomes]
rs798497	0.95[CEU][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes]
rs798498	0.91[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs798499	0.80[CHB][hapmap];0.92[JPT][hapmap]
rs798500	0.95[CEU][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes]
rs798502	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs798506	0.82[EUR][1000 genomes]
rs798508	0.85[EUR][1000 genomes]
rs798511	0.87[EUR][1000 genomes]
rs798512	0.81[JPT][hapmap]
rs798514	0.86[EUR][1000 genomes]
rs798518	0.83[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs798526	0.85[EUR][1000 genomes]
rs798528	0.87[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs798548	0.82[CEU][hapmap]
rs798557	0.88[CHB][hapmap]
rs960273	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	nsv1022612	chr7:2789555-3019200	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1018162	chr7:2817460-2891181	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv538655	chr7:2817460-2891181	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2644312	GNA12	cis	multi-tissue	Pritchard
rs2644312	GNA12	cis	Nerve Tibial	GTEx
rs2644312	GNA12	cis	Artery Tibial	GTEx
rs2644312	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs2644312		cis	Lymphoblastoid	GTEx
rs2644312	LOC392620	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2810600-2842600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:2824000-2842800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:2829800-2841200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr7:2829800-2841400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:2830000-2841200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr7:2830200-2842800	Weak transcription	Colonic Mucosa	Colon
7	chr7:2832000-2841400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:2832800-2842600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr7:2833000-2842400	Weak transcription	Spleen	Spleen
10	chr7:2833200-2842400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:2834200-2841200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr7:2834600-2841400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr7:2834600-2842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:2834600-2847800	Weak transcription	Liver	Liver
15	chr7:2834800-2841400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr7:2834800-2842200	Weak transcription	Brain Germinal Matrix	brain
17	chr7:2834800-2842400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr7:2835000-2841200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr7:2835000-2842200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:2835200-2842400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr7:2836400-2841200	Enhancers	Primary B cells from peripheral blood	blood
22	chr7:2836600-2842400	Weak transcription	Fetal Kidney	kidney
23	chr7:2836600-2844600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:2837000-2841800	Weak transcription	Brain Angular Gyrus	brain
25	chr7:2837000-2842400	Weak transcription	Psoas Muscle	Psoas
26	chr7:2837000-2850600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr7:2837200-2841200	Enhancers	A549	lung
28	chr7:2837600-2841200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr7:2837600-2842200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr7:2838000-2842800	Enhancers	Primary hematopoietic stem cells	blood
31	chr7:2838600-2842200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr7:2838600-2844200	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr7:2838800-2841600	Enhancers	H1 Cell Line	embryonic stem cell
34	chr7:2839000-2841200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr7:2839000-2841400	Enhancers	GM12878-XiMat	blood
36	chr7:2839000-2842200	Enhancers	Fetal Lung	lung
37	chr7:2839400-2841200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr7:2839400-2841200	Enhancers	H9 Cell Line	embryonic stem cell
39	chr7:2839400-2841400	Enhancers	Brain Substantia Nigra	brain
40	chr7:2839400-2843600	Enhancers	Dnd41	blood
41	chr7:2839400-2848600	Enhancers	Fetal Heart	heart
42	chr7:2839400-2850800	Weak transcription	Primary B cells from cord blood	blood
43	chr7:2839600-2841200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:2839600-2841200	Enhancers	Gastric	stomach
45	chr7:2839600-2842200	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr7:2839600-2842600	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr7:2839600-2843400	Enhancers	Fetal Muscle Leg	muscle
48	chr7:2839600-2845000	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr7:2839800-2841200	Enhancers	Left Ventricle	heart
50	chr7:2839800-2841200	Enhancers	Right Atrium	heart

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