Variant report

Variant	rs37979
Chromosome Location	chr7:8019057-8019058
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:8018325-8020900	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:8018316..8019921-chr7:8030363..8032239,2	K562	blood:
2	chr7:8006834..8014864-chr7:8015250..8023851,23	K562	blood:
3	chr7:8007277..8011687-chr7:8017849..8023164,7	MCF-7	breast:
4	chr7:8018021..8019706-chr7:8020925..8023416,2	K562	blood:
5	chr7:8017218..8019521-chr7:8021916..8024291,2	K562	blood:

Variant related genes	Relation type
ENSG00000233264	TF binding region
ENSG00000106415	Chromatin interaction
ENSG00000233108	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10226865	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10238003	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10253861	0.80[AMR][1000 genomes]
rs10264999	0.83[EUR][1000 genomes]
rs10278726	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10278791	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10281919	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11981372	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1476823	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs258850	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs258851	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs258852	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs37976	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs37982	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs37986	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs37987	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs37996	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs37997	0.86[EUR][1000 genomes]
rs38000	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs38007	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs38008	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs38009	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs38015	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4725055	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4725056	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4725059	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6463753	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6953808	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7796831	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7808399	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7810540	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9655516	0.84[AMR][1000 genomes];0.89[EUR][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	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1030180	chr7:7860424-8059221	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv3346837	chr7:7915187-8068557	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1020161	chr7:7929384-8047553	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs37979	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8010800-8023600	Weak transcription	Psoas Muscle	Psoas
2	chr7:8011400-8023600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr7:8012000-8020000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:8012200-8020600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr7:8012800-8019200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr7:8012800-8019600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr7:8012800-8021000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr7:8013400-8029000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr7:8013400-8029600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:8014000-8019600	Enhancers	Primary T cells from cord blood	blood
11	chr7:8014200-8028600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr7:8015000-8045000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:8015200-8031800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:8015800-8023200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:8016600-8019600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr7:8016600-8019600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr7:8016600-8023800	Weak transcription	Small Intestine	intestine
18	chr7:8016600-8026800	Weak transcription	Thymus	Thymus
19	chr7:8016600-8027200	Weak transcription	Fetal Thymus	thymus
20	chr7:8017000-8020400	Enhancers	Fetal Heart	heart
21	chr7:8017000-8020800	ZNF genes & repeats	GM12878-XiMat	blood
22	chr7:8017200-8020000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr7:8017400-8020400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr7:8017600-8019600	Enhancers	Liver	Liver
25	chr7:8017600-8019600	Weak transcription	Left Ventricle	heart
26	chr7:8017600-8024600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr7:8017800-8019200	Weak transcription	Brain Germinal Matrix	brain
28	chr7:8017800-8019400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:8017800-8021000	Weak transcription	Fetal Stomach	stomach
30	chr7:8017800-8021200	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr7:8017800-8023800	Weak transcription	Aorta	Aorta
32	chr7:8017800-8029000	Weak transcription	Hela-S3	cervix
33	chr7:8017800-8029600	Weak transcription	Colon Smooth Muscle	Colon
34	chr7:8017800-8029600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr7:8018000-8020000	Weak transcription	Dnd41	blood
36	chr7:8018000-8029000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr7:8018400-8019200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr7:8018400-8019600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr7:8018400-8020000	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr7:8018400-8022000	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr7:8018400-8022600	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr7:8018600-8019600	Enhancers	Adipose Nuclei	Adipose
43	chr7:8018600-8019600	Enhancers	K562	blood
44	chr7:8018600-8020000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr7:8018600-8020200	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr7:8018800-8019600	Enhancers	Fetal Lung	lung
47	chr7:8018800-8020000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr7:8019000-8019400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr7:8019000-8020200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr7:8019000-8024400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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