Variant report

Variant	rs2644307
Chromosome Location	chr7:2832973-2832974
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:2832115..2834108-chr7:2841664..2843716,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2258709	0.94[ASN][1000 genomes]
rs2527686	0.94[ASN][1000 genomes]
rs2533885	0.89[ASN][1000 genomes]
rs2533886	0.94[ASN][1000 genomes]
rs2533888	0.94[ASN][1000 genomes]
rs2533890	0.91[ASN][1000 genomes]
rs2644306	0.90[ASN][1000 genomes]
rs757786	0.94[ASN][1000 genomes]
rs757787	0.94[ASN][1000 genomes]
rs7790322	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2644307	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs2644307	GNA12	cis	multi-tissue	Pritchard
rs2644307	GNA12	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2803400-2833400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:2810600-2842600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:2810800-2840800	Weak transcription	Stomach Mucosa	stomach
4	chr7:2814400-2838800	Weak transcription	K562	blood
5	chr7:2815800-2840600	Weak transcription	Fetal Brain Male	brain
6	chr7:2822400-2835000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:2822600-2841000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr7:2822800-2834800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:2823600-2835000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:2824000-2842800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr7:2824400-2836600	Weak transcription	Small Intestine	intestine
12	chr7:2824800-2834800	Strong transcription	Fetal Intestine Small	intestine
13	chr7:2824800-2835000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:2825000-2835000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr7:2825000-2835000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr7:2825200-2834800	Strong transcription	NHLF	lung
17	chr7:2825600-2834600	Strong transcription	Fetal Lung	lung
18	chr7:2825600-2835000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr7:2825600-2835000	Strong transcription	HepG2	liver
20	chr7:2825600-2835200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr7:2825600-2835200	Strong transcription	Fetal Muscle Leg	muscle
22	chr7:2825800-2834800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr7:2826000-2835000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:2826200-2835000	Strong transcription	Fetal Intestine Large	intestine
25	chr7:2826400-2833400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr7:2826400-2834800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr7:2826400-2835000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr7:2826400-2835200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr7:2827200-2834800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr7:2827200-2834800	Strong transcription	Fetal Stomach	stomach
31	chr7:2827200-2835400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr7:2827400-2834800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:2828000-2836600	Weak transcription	Psoas Muscle	Psoas
34	chr7:2828400-2835000	Strong transcription	Primary B cells from cord blood	blood
35	chr7:2829000-2835000	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr7:2829200-2834400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:2829200-2834800	Strong transcription	Brain Germinal Matrix	brain
38	chr7:2829200-2835000	Strong transcription	Dnd41	blood
39	chr7:2829600-2833000	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr7:2829600-2834400	Strong transcription	Brain Hippocampus Middle	brain
41	chr7:2829600-2835000	Strong transcription	Fetal Muscle Trunk	muscle
42	chr7:2829800-2834200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr7:2829800-2834600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr7:2829800-2834600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr7:2829800-2834800	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr7:2829800-2835000	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr7:2829800-2835000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr7:2829800-2841200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr7:2829800-2841400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr7:2830000-2834000	Strong transcription	Primary hematopoietic stem cells	blood

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