Variant report

Variant	rs34434107
Chromosome Location	chr4:727153-727154
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:726284..729928-chr4:730296..736157,5	MCF-7	breast:
2	chr4:725258..728014-chr4:756169..758632,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 32 )

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

rs_ID	r²[population]
rs10034650	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10452329	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7376288	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7377200	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7672618	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328756	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	nsv870115	chr4:692811-733794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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

mRNA abundance (count:32)

SNP	Gene	Cis/trans	Tissue	Source
rs34434107	AC139887.4	cis	Stomach	GTEx
rs34434107	RP11-440L14.1	cis	Adipose Subcutaneous	GTEx
rs34434107	PCGF3	cis	Nerve Tibial	GTEx
rs34434107	PCGF3	cis	Skin Sun Exposed Lower leg	GTEx
rs34434107	PCGF3	cis	Adipose Subcutaneous	GTEx
rs34434107	RP11-440L14.1	cis	Esophagus Mucosa	GTEx
rs34434107	RP11-440L14.1	cis	Artery Aorta	GTEx
rs34434107	RP11-440L14.1	cis	Thyroid	GTEx
rs34434107	PCGF3	cis	Thyroid	GTEx
rs34434107	RP11-440L14.1	cis	Skin Sun Exposed Lower leg	GTEx
rs34434107	PCGF3	cis	Esophagus Muscularis	GTEx
rs34434107	AC139887.4	cis	Thyroid	GTEx
rs34434107	PCGF3	cis	Stomach	GTEx
rs34434107	PCGF3	Cis_1M	lymphoblastoid	RTeQTL
rs34434107	RP11-440L14.1	cis	Artery Tibial	GTEx
rs34434107	RP11-440L14.1	cis	Esophagus Muscularis	GTEx
rs34434107	PCGF3	cis	Heart Left Ventricle	GTEx
rs34434107	AC139887.4	cis	Artery Aorta	GTEx
rs34434107	PCGF3	cis	Artery Aorta	GTEx
rs34434107	PCGF3	cis	Esophagus Mucosa	GTEx
rs34434107	RP11-440L14.1	cis	Nerve Tibial	GTEx
rs34434107	PCGF3	cis	Muscle Skeletal	GTEx
rs34434107	RP11-440L14.1	cis	lung	GTEx
rs34434107	PCGF3	cis	lung	GTEx
rs34434107	PCGF3	cis	Artery Tibial	GTEx
rs34434107	AC139887.4	cis	Adipose Subcutaneous	GTEx
rs34434107	AC139887.4	cis	Nerve Tibial	GTEx
rs34434107	RP11-440L14.1	cis	Heart Left Ventricle	GTEx
rs34434107	AC139887.4	cis	Esophagus Muscularis	GTEx
rs34434107	AC139887.4	cis	Skin Sun Exposed Lower leg	GTEx
rs34434107	AC139887.4	cis	Artery Tibial	GTEx
rs34434107	AC139887.4	cis	lung	GTEx

Chromatin state (count:125 , 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	chr4:703600-727200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr4:704600-727600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:708200-736400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr4:713400-727600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:715600-750200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:718400-735400	Weak transcription	Fetal Heart	heart
8	chr4:718600-732600	Weak transcription	Stomach Mucosa	stomach
9	chr4:719000-733000	Strong transcription	Fetal Intestine Small	intestine
10	chr4:720000-738400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:720800-727400	Weak transcription	Psoas Muscle	Psoas
12	chr4:720800-738400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:721000-727400	Weak transcription	NHDF-Ad	bronchial
14	chr4:721000-738600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:721000-743600	Weak transcription	Right Atrium	heart
16	chr4:721800-727400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr4:721800-727400	Weak transcription	Fetal Kidney	kidney
18	chr4:721800-727600	Weak transcription	Fetal Brain Male	brain
19	chr4:721800-728600	Weak transcription	Small Intestine	intestine
20	chr4:722000-736000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:723200-735800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr4:723600-727200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:723600-733400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:723600-735800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr4:723600-736400	Strong transcription	Fetal Brain Female	brain
26	chr4:723600-738600	Strong transcription	Brain Germinal Matrix	brain
27	chr4:723800-730200	Strong transcription	Pancreas	Pancrea
28	chr4:723800-734600	Strong transcription	Right Ventricle	heart
29	chr4:723800-735000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:723800-735800	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:723800-736200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:723800-737600	Strong transcription	Dnd41	blood
33	chr4:723800-738400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr4:724000-729800	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr4:724000-735800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr4:724200-732400	Strong transcription	Colon Smooth Muscle	Colon
37	chr4:724200-732400	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr4:724200-734800	Strong transcription	Gastric	stomach
39	chr4:724200-735000	Strong transcription	Left Ventricle	heart
40	chr4:724200-738600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:724200-738600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:724400-727600	Strong transcription	A549	lung
43	chr4:724400-730000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr4:724400-732000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr4:724400-732000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr4:724400-732200	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr4:724400-732200	Strong transcription	Aorta	Aorta
48	chr4:724400-732400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr4:724400-732600	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr4:724400-732800	Strong transcription	Rectal Mucosa Donor 29	rectum

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