Variant report

Variant	rs3784120
Chromosome Location	chr14:68875251-68875252
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr14:68875098-68875977	GM12878	blood:	n/a	n/a
2	CTCF	chr14:68875120-68875270	AG09309	skin:	n/a	n/a
3	RUNX3	chr14:68874859-68875940	GM12878	blood:	n/a	chr14:68875131-68875148

No.	Distal block	Cell Line	Cell type
1	chr14:68717908..68718808-chr14:68875069..68875621,2	MCF-7	breast:
2	chr14:68874787..68877042-chr14:69256947..69261262,5	MCF-7	breast:
3	chr14:68874422..68876560-chr14:68917210..68919042,2	MCF-7	breast:
4	chr14:68875187..68876826-chr14:69253735..69255769,2	MCF-7	breast:
5	chr14:68764605..68765199-chr14:68875194..68875820,2	MCF-7	breast:

Variant related genes	Relation type
RAD51B	TF binding region
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1006816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10146321	0.80[MEX][hapmap]
rs10146772	0.91[CHB][hapmap];0.82[GIH][hapmap]
rs10150212	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11158734	0.81[ASN][1000 genomes]
rs11158735	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11158736	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158743	0.90[MEX][hapmap]
rs11625452	0.84[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs12435046	0.90[ASN][1000 genomes]
rs12717531	0.90[MEX][hapmap]
rs12889666	0.91[CEU][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap]
rs12889770	0.91[CEU][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.82[ASN][1000 genomes]
rs12894080	0.80[MEX][hapmap]
rs1885014	0.84[CHD][hapmap]
rs1956536	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1956537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2025009	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs2331696	0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2877461	0.84[CHD][hapmap]
rs3784115	0.86[CHD][hapmap]
rs3784116	0.86[JPT][hapmap]
rs3784117	0.90[MEX][hapmap]
rs3784119	0.87[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs3950069	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs4902576	0.91[CEU][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4902577	0.91[CEU][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs55665241	0.89[ASN][1000 genomes]
rs61039700	0.80[ASN][1000 genomes]
rs8012610	0.86[CHB][hapmap]
rs8014025	0.85[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs8014234	0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs8018477	0.84[CHD][hapmap]
rs8021199	0.81[JPT][hapmap]
rs927221	0.83[CEU][hapmap]
rs9323508	0.82[CHB][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	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv832822	chr14:68874640-69060272	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3784120	ZFYVE26	cis	cerebellum	SCAN
rs3784120	FAM71D	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68863600-68877200	Enhancers	Primary B cells from peripheral blood	blood
2	chr14:68864800-68878000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr14:68865000-68877000	Weak transcription	Pancreas	Pancrea
4	chr14:68867200-68876200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr14:68867200-68876400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr14:68867200-68886400	Weak transcription	Dnd41	blood
7	chr14:68868200-68887200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr14:68868400-68876000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr14:68870600-68875600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr14:68870800-68876000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr14:68870800-68877400	Enhancers	Primary B cells from cord blood	blood
12	chr14:68871200-68875600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr14:68871600-68876000	Weak transcription	Adipose Nuclei	Adipose
14	chr14:68871800-68875600	Weak transcription	Fetal Muscle Leg	muscle
15	chr14:68871800-68875800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr14:68871800-68876000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr14:68871800-68876000	Weak transcription	Fetal Heart	heart
18	chr14:68871800-68876200	Weak transcription	Ovary	ovary
19	chr14:68871800-68876200	Weak transcription	Spleen	Spleen
20	chr14:68871800-68879000	Weak transcription	NH-A	brain
21	chr14:68871800-68880800	Weak transcription	Fetal Lung	lung
22	chr14:68872200-68875600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr14:68872200-68876200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr14:68872200-68877000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr14:68872200-68877200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr14:68872200-68883400	Weak transcription	Esophagus	oesophagus
27	chr14:68872800-68879400	Weak transcription	HUVEC	blood vessel
28	chr14:68873200-68876800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr14:68873400-68876000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr14:68873400-68878800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr14:68873400-68878800	Weak transcription	NHEK	skin
32	chr14:68873400-68883800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr14:68873600-68875400	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr14:68874200-68875400	Enhancers	Fetal Intestine Small	intestine
35	chr14:68874200-68875400	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr14:68874200-68876400	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr14:68874200-68876600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr14:68874200-68876600	Enhancers	GM12878-XiMat	blood
39	chr14:68874200-68879200	Enhancers	A549	lung
40	chr14:68874400-68875400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr14:68874400-68875800	Enhancers	HMEC	breast
42	chr14:68874400-68876400	Enhancers	Primary T cells fromperipheralblood	blood
43	chr14:68874400-68877000	Enhancers	Primary T cells from cord blood	blood
44	chr14:68874600-68875600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr14:68874600-68875800	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr14:68874600-68875800	Enhancers	Fetal Thymus	thymus
47	chr14:68874600-68876600	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr14:68874600-68876600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr14:68874600-68877200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr14:68874600-68879000	Weak transcription	Duodenum Mucosa	Duodenum

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