Variant report

Variant	rs1986756
Chromosome Location	chr7:30651938-30651939
allele	C/T
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	MAFK	chr7:30651853-30651995	HepG2	liver:	n/a	n/a
2	MAFK	chr7:30651806-30652045	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:30651451-30653445	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr7:30651919-30652163	K562	blood:	n/a	n/a
5	POLR2A	chr7:30651424-30654230	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:30651311..30653925-chr7:30670697..30673302,2	K562	blood:
2	chr7:30645240..30648222-chr7:30649750..30651957,2	MCF-7	breast:
3	chr7:30645076..30647413-chr7:30649559..30652192,3	MCF-7	breast:

Variant related genes	Relation type
GARS	TF binding region
ENSG00000106105	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1049402	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2529437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2709787	0.96[ASN][1000 genomes]
rs2709809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38441	0.86[CHB][hapmap]
rs38442	0.85[CHB][hapmap]
rs38466	0.82[CHB][hapmap]
rs38467	0.82[CHB][hapmap]
rs38468	0.82[CHB][hapmap]
rs38469	0.83[CHB][hapmap]
rs38471	0.82[CHB][hapmap]
rs38484	0.81[ASN][1000 genomes]
rs38485	0.94[ASN][1000 genomes]
rs38486	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs38487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs38488	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs38489	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs38493	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs38494	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs38495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38497	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs38498	0.96[ASN][1000 genomes]
rs39738	0.82[CHB][hapmap]
rs4258	0.82[CHB][hapmap]
rs973002	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs975537	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538811	chr7:30549595-31405593	Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1016256	chr7:30649212-31163056	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs1986756	AC005154.6	cis	Heart Left Ventricle	GTEx
rs1986756	AC005154.6	cis	Whole Blood	GTEx
rs1986756	AC005154.6	cis	Thyroid	GTEx
rs1986756	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs1986756	AC005154.6	cis	Artery Aorta	GTEx
rs1986756	AC005154.6	cis	Esophagus Muscularis	GTEx
rs1986756	AC005154.6	cis	Muscle Skeletal	GTEx
rs1986756	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs1986756	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs1986756	AC005154.6	cis	lung	GTEx
rs1986756	AC005154.6	cis	Nerve Tibial	GTEx
rs1986756	AC005154.6	cis	Artery Tibial	GTEx
rs1986756	AC005154.8	cis	Whole Blood	GTEx
rs1986756	AC005154.6	cis	Esophagus Mucosa	GTEx
rs1986756	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs1986756	AC005154.6	cis	Stomach	GTEx
rs1986756	LOC401320	cis	uninvolved skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30636000-30655600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:30636200-30689200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:30636600-30655800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:30636600-30661600	Weak transcription	Fetal Heart	heart
5	chr7:30636600-30682800	Weak transcription	Stomach Mucosa	stomach
6	chr7:30637000-30676000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr7:30637200-30653000	Strong transcription	HSMM	muscle
8	chr7:30637200-30676200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:30637600-30653000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr7:30637600-30675400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:30637600-30675400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:30637800-30675600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr7:30638000-30675800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr7:30638000-30675800	Strong transcription	A549	lung
15	chr7:30638000-30676000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:30638000-30676200	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr7:30638200-30653000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:30638200-30675800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:30638200-30675800	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr7:30638200-30675800	Strong transcription	Fetal Thymus	thymus
21	chr7:30638200-30676000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr7:30638200-30676000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr7:30638400-30652600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:30638400-30654400	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr7:30638400-30654400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr7:30638400-30655400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr7:30638400-30664000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr7:30638400-30675800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr7:30638400-30675800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr7:30638400-30676000	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr7:30638400-30676000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:30638400-30676000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr7:30638400-30676000	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr7:30638400-30676000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr7:30638400-30676000	Strong transcription	Liver	Liver
36	chr7:30638400-30676200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:30638600-30652200	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr7:30638600-30652600	Strong transcription	HMEC	breast
39	chr7:30638600-30656800	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr7:30638600-30675800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr7:30638600-30675800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr7:30638600-30676000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr7:30638800-30652000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr7:30638800-30672800	Strong transcription	NHDF-Ad	bronchial
45	chr7:30638800-30675200	Strong transcription	K562	blood
46	chr7:30638800-30675600	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr7:30639000-30652800	Strong transcription	HepG2	liver
48	chr7:30639000-30669600	Strong transcription	Fetal Intestine Large	intestine
49	chr7:30639000-30676200	Strong transcription	Hela-S3	cervix
50	chr7:30639200-30664200	Strong transcription	Duodenum Mucosa	Duodenum

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