Variant report

Variant	rs7778571
Chromosome Location	chr7:99664817-99664818
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99661987..99666406-chr7:99667743..99671681,6	MCF-7	breast:
2	chr7:99654361..99659612-chr7:99660293..99666807,10	K562	blood:
3	chr7:99611961..99615773-chr7:99661175..99666298,6	K562	blood:
4	chr7:99621050..99622719-chr7:99664810..99666515,2	MCF-7	breast:
5	chr7:99661710..99665437-chr7:99677979..99680889,6	MCF-7	breast:
6	chr7:99644359..99647812-chr7:99662210..99665562,4	K562	blood:

Variant related genes	Relation type
ENSG00000166526	Chromatin interaction
ENSG00000166529	Chromatin interaction
ENSG00000106261	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10231522	1.00[ASN][1000 genomes]
rs17161997	1.00[CHB][hapmap]

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	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7778571	MYL10	cis	cerebellum	SCAN
rs7778571	ZNF3	cis	parietal	SCAN
rs7778571	C7orf59	cis	brain	BrainEAC
rs7778571	ZSCAN21	cis	parietal	SCAN
rs7778571	AP4M1	cis	multi-tissue	Pritchard
rs7778571	AP4M1	Cis_1M	lymphoblastoid	RTeQTL
rs7778571	AP4M1	cis	lymphoblastoid	seeQTL
rs7778571	PMPCB	cis	parietal	SCAN
rs7778571	TAF6	cis	Liver	GTEx
rs7778571	TAF6	cis	multi-tissue	Pritchard
rs7778571	AP4M1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99648400-99667600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:99648400-99667600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:99648400-99667600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr7:99648400-99667800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr7:99648400-99668000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr7:99653400-99666400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:99653800-99667600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:99654000-99668000	Strong transcription	Fetal Brain Female	brain
9	chr7:99654200-99666400	Strong transcription	Fetal Intestine Small	intestine
10	chr7:99654200-99667400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr7:99654400-99667600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:99654400-99667600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:99654400-99667600	Strong transcription	Brain Germinal Matrix	brain
14	chr7:99654400-99668400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:99654600-99665600	Strong transcription	Dnd41	blood
16	chr7:99654600-99667600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:99654600-99667600	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr7:99654600-99667800	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr7:99656200-99667400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr7:99656200-99668000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr7:99657000-99665800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr7:99658400-99665400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr7:99658400-99667600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr7:99659200-99667200	Strong transcription	Fetal Muscle Trunk	muscle
25	chr7:99661000-99666800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:99661600-99675200	ZNF genes & repeats	A549	lung
27	chr7:99662200-99665600	Strong transcription	HSMM	muscle
28	chr7:99662200-99667200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr7:99662200-99667600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr7:99662200-99667600	Weak transcription	HUVEC	blood vessel
31	chr7:99662200-99668400	Weak transcription	Small Intestine	intestine
32	chr7:99662400-99666800	Weak transcription	GM12878-XiMat	blood
33	chr7:99662400-99667200	Weak transcription	Psoas Muscle	Psoas
34	chr7:99662400-99667200	Weak transcription	NHEK	skin
35	chr7:99662400-99667400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr7:99662400-99667400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr7:99662400-99667400	Weak transcription	HMEC	breast
38	chr7:99662400-99667600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr7:99662400-99667600	Weak transcription	Colonic Mucosa	Colon
40	chr7:99662600-99666600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr7:99662600-99667000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr7:99662600-99667000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr7:99662600-99667200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr7:99662600-99667400	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr7:99662600-99667400	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr7:99662600-99667400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr7:99662600-99667400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr7:99662600-99667400	Weak transcription	Osteobl	bone
49	chr7:99662600-99667600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr7:99662600-99667600	Weak transcription	Primary B cells from peripheral blood	blood

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