Variant report

Variant	rs3734969
Chromosome Location	chr7:128866389-128866390
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:128865235..128868002-chr7:128877453..128879844,2	MCF-7	breast:
2	chr7:128865013..128866542-chr7:128952036..128953985,2	MCF-7	breast:
3	chr7:128864343..128867175-chr7:129072018..129074296,2	K562	blood:
4	chr7:128866260..128868499-chr7:128899979..128902017,2	K562	blood:
5	chr7:128694449..128696467-chr7:128864942..128866484,2	K562	blood:
6	chr7:128694062..128696467-chr7:128864942..128866876,2	K562	blood:

Variant related genes	Relation type
ENSG00000230359	Chromatin interaction
ENSG00000128578	Chromatin interaction
ENSG00000064419	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12154376	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17168214	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2694571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2694586	0.80[AFR][1000 genomes]
rs2694590	0.80[AFR][1000 genomes]
rs2718098	0.80[AFR][1000 genomes]
rs4731565	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6969620	0.94[LWK][hapmap];0.93[YRI][hapmap]

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	nsv831127	chr7:128716256-128874691	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1031284	chr7:128866118-128910506	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3734969	PLXNA4	cis	parietal	SCAN
rs3734969	KCP	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128863600-128867200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:128863800-128866400	Active TSS	NHDF-Ad	bronchial
3	chr7:128863800-128866600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr7:128863800-128866600	Active TSS	H1 Cell Line	embryonic stem cell
5	chr7:128864000-128866400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr7:128864000-128866400	Active TSS	Placenta	Placenta
7	chr7:128864000-128866400	Active TSS	Psoas Muscle	Psoas
8	chr7:128864000-128866600	Active TSS	H9 Cell Line	embryonic stem cell
9	chr7:128864000-128866600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:128864000-128866600	Active TSS	Brain Germinal Matrix	brain
11	chr7:128864200-128866400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr7:128864200-128866400	Active TSS	Brain Cingulate Gyrus	brain
13	chr7:128864200-128866400	Active TSS	Fetal Intestine Large	intestine
14	chr7:128864200-128866400	Active TSS	HMEC	breast
15	chr7:128864200-128866600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:128864200-128866600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:128864200-128866600	Active TSS	Brain Substantia Nigra	brain
18	chr7:128864200-128866600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr7:128864200-128866600	Active TSS	NHLF	lung
20	chr7:128865000-128866600	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr7:128865200-128866400	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr7:128865400-128866400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr7:128865400-128866400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr7:128865400-128866400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:128865400-128866400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:128865400-128866600	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr7:128865400-128866800	Flanking Active TSS	Dnd41	blood
28	chr7:128865600-128866400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr7:128865600-128866400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr7:128865600-128866400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr7:128865600-128866400	Flanking Active TSS	Liver	Liver
32	chr7:128865600-128866400	Flanking Active TSS	Fetal Kidney	kidney
33	chr7:128865600-128866400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr7:128865600-128866400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr7:128865600-128866400	Flanking Active TSS	K562	blood
36	chr7:128865600-128866400	Flanking Active TSS	Osteobl	bone
37	chr7:128865600-128866600	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr7:128865600-128866600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr7:128865600-128866600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:128865600-128866600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr7:128865600-128866600	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr7:128865600-128866600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr7:128865600-128866600	Flanking Active TSS	HUVEC	blood vessel
44	chr7:128865600-128866800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr7:128865600-128866800	Flanking Active TSS	Fetal Brain Female	brain
46	chr7:128865800-128866400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr7:128865800-128866400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr7:128865800-128866400	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr7:128865800-128866400	Flanking Active TSS	A549	lung
50	chr7:128865800-128866600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell

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