Variant report

Variant	rs7376288
Chromosome Location	chr4:741742-741743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:736509..739809-chr4:741556..745067,3	MCF-7	breast:
2	chr4:741073..743262-chr4:744150..746174,2	K562	blood:
3	chr4:741180..743978-chr4:986881..988849,2	MCF-7	breast:
4	chr4:732543..739360-chr4:740100..745945,6	K562	blood:
5	chr4:735427..738255-chr4:740119..742339,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185619	Chromatin interaction
ENSG00000145217	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 31 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10034650	0.85[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10452329	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.84[ASN][1000 genomes]
rs34434107	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7377200	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7672618	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9328756	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
6	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
10	esv1829397	chr4:655939-1041957	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
11	nsv829834	chr4:665477-775524	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
12	nsv593209	chr4:686563-747810	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	esv1833383	chr4:708887-753697	Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv878253	chr4:708932-771587	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
15	nsv878254	chr4:708932-899143	Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv878255	chr4:708932-1052488	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
17	nsv878256	chr4:712222-744098	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
18	nsv878257	chr4:712222-852313	Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
19	nsv878258	chr4:712222-1058358	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
20	nsv878259	chr4:713920-852313	Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
21	nsv878260	chr4:713920-1052488	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
22	nsv4195	chr4:727187-768059	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
23	nsv10416	chr4:737736-742329	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
24	esv3512383	chr4:738190-741970	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
25	esv3512384	chr4:738190-741970	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
26	esv3407630	chr4:738302-741800	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
27	esv3468300	chr4:738302-742000	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
28	esv3468301	chr4:738302-742000	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
29	esv1833385	chr4:738603-753697	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:31)

SNP	Gene	Cis/trans	Tissue	Source
rs7376288	RP11-440L14.1	cis	Heart Left Ventricle	GTEx
rs7376288	PCGF3	cis	Esophagus Muscularis	GTEx
rs7376288	AC139887.4	cis	Artery Tibial	GTEx
rs7376288	PCGF3	cis	Nerve Tibial	GTEx
rs7376288	PCGF3	Cis_1M	lymphoblastoid	RTeQTL
rs7376288	RP11-440L14.1	cis	Artery Tibial	GTEx
rs7376288	AC139887.4	cis	lung	GTEx
rs7376288	RP11-440L14.1	cis	Esophagus Muscularis	GTEx
rs7376288	AC139887.4	cis	Stomach	GTEx
rs7376288	PCGF3	cis	Heart Left Ventricle	GTEx
rs7376288	AC139887.4	cis	Adipose Subcutaneous	GTEx
rs7376288	RP11-440L14.1	cis	Artery Aorta	GTEx
rs7376288	AC139887.4	cis	Thyroid	GTEx
rs7376288	RP11-440L14.1	cis	lung	GTEx
rs7376288	PCGF3	cis	Artery Aorta	GTEx
rs7376288	RP11-440L14.1	cis	Thyroid	GTEx
rs7376288	AC139887.4	cis	Skin Sun Exposed Lower leg	GTEx
rs7376288	PCGF3	cis	Esophagus Mucosa	GTEx
rs7376288	RP11-440L14.1	cis	Nerve Tibial	GTEx
rs7376288	PCGF3	cis	Adipose Subcutaneous	GTEx
rs7376288	PCGF3	cis	Artery Tibial	GTEx
rs7376288	RP11-440L14.1	cis	Esophagus Mucosa	GTEx
rs7376288	PCGF3	cis	Thyroid	GTEx
rs7376288	PCGF3	cis	Stomach	GTEx
rs7376288	PCGF3	cis	lung	GTEx
rs7376288	AC139887.4	cis	Nerve Tibial	GTEx
rs7376288	RP11-440L14.1	cis	Adipose Subcutaneous	GTEx
rs7376288	AC139887.4	cis	Artery Aorta	GTEx
rs7376288	PCGF3	cis	Skin Sun Exposed Lower leg	GTEx
rs7376288	PCGF3	cis	Muscle Skeletal	GTEx
rs7376288	RP11-440L14.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:702200-754800	Weak transcription	Hela-S3	cervix
2	chr4:715600-750200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:721000-743600	Weak transcription	Right Atrium	heart
4	chr4:727000-767600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:728000-741800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr4:728600-755800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr4:728600-763400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr4:729000-742400	Weak transcription	Small Intestine	intestine
9	chr4:729000-754600	Weak transcription	Fetal Kidney	kidney
10	chr4:729000-762600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:729600-753800	Weak transcription	Psoas Muscle	Psoas
12	chr4:729600-760800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr4:732000-742400	Weak transcription	NHDF-Ad	bronchial
14	chr4:732000-745200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr4:732200-741800	Weak transcription	K562	blood
16	chr4:732200-743600	Weak transcription	HMEC	breast
17	chr4:733600-742600	Weak transcription	Stomach Mucosa	stomach
18	chr4:733600-753800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:733800-747400	Weak transcription	Primary B cells from cord blood	blood
20	chr4:734000-744000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:734000-745400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr4:734200-741800	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:734200-744800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr4:734400-741800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr4:734400-745400	Weak transcription	Brain Hippocampus Middle	brain
26	chr4:734600-741800	Weak transcription	A549	lung
27	chr4:734800-741800	Weak transcription	Brain Substantia Nigra	brain
28	chr4:734800-742000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr4:734800-744200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr4:734800-745600	Weak transcription	Brain Anterior Caudate	brain
31	chr4:735000-741800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr4:735000-743600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:735000-743800	Weak transcription	Colonic Mucosa	Colon
34	chr4:735200-742000	Weak transcription	Esophagus	oesophagus
35	chr4:735200-742000	Weak transcription	HUVEC	blood vessel
36	chr4:735200-742400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr4:735200-745200	Weak transcription	Fetal Brain Male	brain
38	chr4:735200-745400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:736600-752000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr4:736800-741800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:736800-742200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr4:738000-742400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr4:738000-742400	Weak transcription	HepG2	liver
44	chr4:738200-742400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:738400-741800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr4:738400-741800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr4:738400-742000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:738400-742200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:738400-742200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr4:738400-743600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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