Variant report

Variant	rs6447971
Chromosome Location	chr4:20724027-20724028
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:20701205..20703695-chr4:20723209..20725454,2	MCF-7	breast:
2	chr4:20700788..20703573-chr4:20723140..20724857,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163138	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10031524	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10938803	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11936560	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940062	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1820505	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114474	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2322687	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3764965	0.85[EUR][1000 genomes]
rs3816874	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4577580	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55874299	0.80[EUR][1000 genomes]
rs61428210	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6447972	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447973	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6811933	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6857386	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6858843	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7662488	0.81[ASN][1000 genomes]
rs7663837	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7668797	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688592	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689421	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7694208	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs964019	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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	nsv1013077	chr4:20599841-20732558	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6447971	PACRGL	cis	lung	GTEx
rs6447971	C4orf28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20703000-20741400	Weak transcription	Stomach Mucosa	stomach
2	chr4:20703200-20741000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:20706800-20738600	Weak transcription	Psoas Muscle	Psoas
4	chr4:20707200-20739400	Weak transcription	HepG2	liver
5	chr4:20708200-20733600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:20709400-20724200	Weak transcription	HUVEC	blood vessel
7	chr4:20715400-20738600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:20715400-20739400	Weak transcription	Osteobl	bone
9	chr4:20717800-20724200	Weak transcription	NH-A	brain
10	chr4:20718000-20738600	Weak transcription	NHDF-Ad	bronchial
11	chr4:20718200-20738400	Weak transcription	Fetal Heart	heart
12	chr4:20721600-20727600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:20721800-20724400	ZNF genes & repeats	Fetal Brain Female	brain
14	chr4:20721800-20724800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:20721800-20724800	Strong transcription	Rectal Smooth Muscle	rectum
16	chr4:20721800-20725200	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr4:20721800-20725600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:20721800-20736000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:20721800-20736400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:20721800-20737200	Strong transcription	Liver	Liver
21	chr4:20722000-20724400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr4:20722000-20724400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:20722000-20724400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr4:20722000-20724600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:20722000-20724600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:20722000-20724600	Strong transcription	Fetal Kidney	kidney
27	chr4:20722000-20724800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
28	chr4:20722000-20724800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
29	chr4:20722000-20724800	Strong transcription	Primary T cells from cord blood	blood
30	chr4:20722000-20724800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:20722000-20724800	ZNF genes & repeats	Fetal Muscle Leg	muscle
32	chr4:20722000-20725000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:20722000-20725000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr4:20722000-20725200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
35	chr4:20722000-20725400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:20722000-20725600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
37	chr4:20722000-20726000	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr4:20722000-20727000	Strong transcription	Brain Cingulate Gyrus	brain
39	chr4:20722000-20727800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr4:20722200-20724200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
41	chr4:20722200-20724400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr4:20722200-20724400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:20722200-20724400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
44	chr4:20722200-20724400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
45	chr4:20722200-20724400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
46	chr4:20722200-20724800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
47	chr4:20722200-20724800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr4:20722200-20725400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:20722200-20727600	Strong transcription	Brain Hippocampus Middle	brain
50	chr4:20722600-20724400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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