Variant report

Variant	rs37978
Chromosome Location	chr7:8017851-8017852
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	MEF2A	chr7:8017417-8017889	K562	blood:	n/a	chr7:8017631-8017648 chr7:8017801-8017822 chr7:8017632-8017648 chr7:8017635-8017644 chr7:8017632-8017647 chr7:8017699-8017720 chr7:8017706-8017717 chr7:8017801-8017822 chr7:8017633-8017648 chr7:8017805-8017816 chr7:8017632-8017647 chr7:8017803-8017817 chr7:8017634-8017645 chr7:8017802-8017818 chr7:8017635-8017646 chr7:8017628-8017649 chr7:8017633-8017647 chr7:8017803-8017818 chr7:8017699-8017720
2	POLR2A	chr7:8017362-8017885	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:8016755..8018272-chr7:8032373..8035088,2	K562	blood:
2	chr7:8016682..8018691-chr7:8023208..8025599,2	MCF-7	breast:
3	chr7:8016338..8018811-chr7:8026553..8029436,2	MCF-7	breast:
4	chr7:8006834..8014864-chr7:8015250..8023851,23	K562	blood:
5	chr7:8007277..8011687-chr7:8017849..8023164,7	MCF-7	breast:
6	chr7:8017218..8019521-chr7:8021916..8024291,2	K562	blood:

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

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10226050	0.81[EUR][1000 genomes]
rs10229643	0.81[EUR][1000 genomes]
rs10258788	0.84[EUR][1000 genomes]
rs10486205	0.83[EUR][1000 genomes]
rs258853	0.84[EUR][1000 genomes]
rs28488572	0.82[EUR][1000 genomes]
rs28670736	0.85[EUR][1000 genomes]
rs37974	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs37975	0.84[EUR][1000 genomes]
rs37977	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs37981	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs37983	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs37988	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs37992	0.86[EUR][1000 genomes]
rs37994	0.86[EUR][1000 genomes]
rs37995	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs37998	0.88[EUR][1000 genomes]
rs37999	0.88[EUR][1000 genomes]
rs38001	0.82[EUR][1000 genomes]
rs38002	0.87[EUR][1000 genomes]
rs38003	0.87[EUR][1000 genomes]
rs38004	0.81[EUR][1000 genomes]
rs38010	0.83[EUR][1000 genomes]
rs38011	0.87[EUR][1000 genomes]
rs38012	0.87[EUR][1000 genomes]
rs38013	0.88[EUR][1000 genomes]
rs38014	0.87[EUR][1000 genomes]
rs38016	0.84[EUR][1000 genomes]
rs38017	0.85[EUR][1000 genomes]
rs38018	0.81[EUR][1000 genomes]
rs38019	0.81[EUR][1000 genomes]
rs38021	0.82[EUR][1000 genomes]
rs38022	0.84[EUR][1000 genomes]
rs38023	0.84[EUR][1000 genomes]
rs62433404	0.85[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
rs37978	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 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	chr7:8012000-8018600	Weak transcription	Adipose Nuclei	Adipose
4	chr7:8012000-8018800	Weak transcription	Fetal Lung	lung
5	chr7:8012000-8020000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr7:8012200-8018000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr7:8012200-8018000	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr7:8012200-8018400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:8012200-8020600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:8012400-8018200	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr7:8012800-8019200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr7:8012800-8019600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr7:8012800-8021000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr7:8013200-8018000	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr7:8013400-8018000	Enhancers	Dnd41	blood
16	chr7:8013400-8029000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr7:8013400-8029600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:8014000-8018000	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr7:8014000-8019600	Enhancers	Primary T cells from cord blood	blood
20	chr7:8014200-8028600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr7:8015000-8045000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:8015200-8031800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:8015800-8023200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:8016600-8019600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr7:8016600-8019600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:8016600-8023800	Weak transcription	Small Intestine	intestine
27	chr7:8016600-8026800	Weak transcription	Thymus	Thymus
28	chr7:8016600-8027200	Weak transcription	Fetal Thymus	thymus
29	chr7:8016800-8018000	Enhancers	Osteobl	bone
30	chr7:8017000-8020400	Enhancers	Fetal Heart	heart
31	chr7:8017000-8020800	ZNF genes & repeats	GM12878-XiMat	blood
32	chr7:8017200-8020000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr7:8017400-8018000	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr7:8017400-8018000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr7:8017400-8018000	Enhancers	Rectal Smooth Muscle	rectum
36	chr7:8017400-8018000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr7:8017400-8020400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr7:8017600-8018600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr7:8017600-8018800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr7:8017600-8019600	Enhancers	Liver	Liver
41	chr7:8017600-8019600	Weak transcription	Left Ventricle	heart
42	chr7:8017600-8024600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr7:8017800-8018200	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr7:8017800-8018600	Weak transcription	K562	blood
45	chr7:8017800-8018800	Weak transcription	Primary B cells from cord blood	blood
46	chr7:8017800-8018800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr7:8017800-8019200	Weak transcription	Brain Germinal Matrix	brain
48	chr7:8017800-8019400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr7:8017800-8021000	Weak transcription	Fetal Stomach	stomach
50	chr7:8017800-8021200	Enhancers	Primary neutrophils fromperipheralblood	blood

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