Variant report

Variant	rs1638738
Chromosome Location	chr7:66055259-66055260
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	chr7:66054686..66058308-chr7:66092199..66095155,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243335	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1267814	0.85[EUR][1000 genomes]
rs13311962	0.85[EUR][1000 genomes]
rs1638724	0.85[EUR][1000 genomes]
rs1638728	0.80[EUR][1000 genomes]
rs1638732	0.81[EUR][1000 genomes]
rs1638735	0.83[EUR][1000 genomes]
rs1796217	0.83[EUR][1000 genomes]
rs1796218	0.82[EUR][1000 genomes]
rs1796219	0.82[EUR][1000 genomes]
rs1796226	0.83[EUR][1000 genomes]
rs1796227	0.83[EUR][1000 genomes]
rs2533283	0.80[EUR][1000 genomes]
rs2533284	0.80[EUR][1000 genomes]
rs2707851	0.83[EUR][1000 genomes]
rs6460311	0.82[EUR][1000 genomes]
rs801199	0.85[EUR][1000 genomes]
rs801210	0.85[EUR][1000 genomes]
rs801212	0.85[EUR][1000 genomes]
rs801213	0.85[EUR][1000 genomes]
rs964971	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv482441	chr7:65885824-66061788	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv970868	chr7:66035219-66056610	Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3367991	chr7:66052417-66055415	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1638738	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs1638738	GS1-124K5.4	cis	Stomach	GTEx
rs1638738	GS1-124K5.11	cis	Thyroid	GTEx
rs1638738	GTF2IRD1P1	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66008600-66056000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:66021800-66056400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:66023200-66055400	Weak transcription	Fetal Brain Male	brain
4	chr7:66024200-66055400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr7:66024200-66055600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:66037600-66056400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:66038000-66056200	Weak transcription	Colonic Mucosa	Colon
8	chr7:66038200-66055400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr7:66038200-66055800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr7:66038400-66055400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr7:66038800-66055400	Weak transcription	Fetal Lung	lung
12	chr7:66039400-66055400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr7:66039400-66055400	Weak transcription	Fetal Kidney	kidney
14	chr7:66039400-66055400	Weak transcription	HUVEC	blood vessel
15	chr7:66039400-66055400	Weak transcription	NH-A	brain
16	chr7:66039800-66055400	Weak transcription	HSMMtube	muscle
17	chr7:66040200-66056200	Weak transcription	Aorta	Aorta
18	chr7:66042000-66055800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr7:66043000-66055400	Weak transcription	GM12878-XiMat	blood
20	chr7:66045200-66055800	Weak transcription	Brain Angular Gyrus	brain
21	chr7:66046400-66055400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr7:66049000-66055400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:66049000-66055400	Weak transcription	Thymus	Thymus
24	chr7:66049000-66055600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr7:66049000-66055800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr7:66049000-66056200	Weak transcription	Left Ventricle	heart
27	chr7:66049200-66055400	Weak transcription	A549	lung
28	chr7:66049200-66055600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr7:66049200-66055600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:66049200-66055800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr7:66049400-66055400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr7:66049400-66055400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr7:66049400-66055800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr7:66049800-66055400	Weak transcription	NHLF	lung
35	chr7:66050200-66055400	Enhancers	Colon Smooth Muscle	Colon
36	chr7:66050400-66056200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr7:66051000-66055400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr7:66051200-66055400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr7:66051800-66055800	Weak transcription	Brain Substantia Nigra	brain
40	chr7:66052200-66055400	Weak transcription	Brain Hippocampus Middle	brain
41	chr7:66052200-66056000	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr7:66052400-66055600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr7:66052400-66056200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr7:66052600-66055400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr7:66052600-66055400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr7:66052800-66055400	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr7:66052800-66055600	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr7:66052800-66055800	Weak transcription	Primary B cells from cord blood	blood
49	chr7:66052800-66056200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr7:66053200-66055400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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