Variant report

Variant	rs1614170
Chromosome Location	chr15:42239405-42239406
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42229163..42231436-chr15:42239273..42241169,2	MCF-7	breast:
2	chr15:42237041..42240876-chr15:42263430..42266549,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246740	Chromatin interaction
ENSG00000103966	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12101888	0.91[CEU][hapmap];0.91[MEX][hapmap]
rs1648854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1648855	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17739167	0.87[MEX][hapmap]
rs4924590	0.91[CEU][hapmap];0.85[AMR][1000 genomes]
rs4924592	0.84[CHB][hapmap];0.82[GIH][hapmap]

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	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1038933	chr15:42138456-42309087	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
5	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv1054728	chr15:42177772-42310009	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1614170	EHD4	cis	cerebellum	SCAN
rs1614170	LCMT2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42222200-42249800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr15:42223200-42243800	Weak transcription	Brain Substantia Nigra	brain
3	chr15:42227400-42243200	Weak transcription	Stomach Mucosa	stomach
4	chr15:42227600-42249200	Weak transcription	Small Intestine	intestine
5	chr15:42230000-42243200	Weak transcription	Brain Hippocampus Middle	brain
6	chr15:42230000-42248400	Strong transcription	GM12878-XiMat	blood
7	chr15:42230000-42249600	Weak transcription	K562	blood
8	chr15:42230400-42262200	Weak transcription	Thymus	Thymus
9	chr15:42230600-42239800	Genic enhancers	HUVEC	blood vessel
10	chr15:42230600-42240000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:42230800-42247000	Weak transcription	Fetal Thymus	thymus
12	chr15:42230800-42249400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:42231000-42240000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr15:42231200-42242600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr15:42231200-42244600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:42231200-42249800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr15:42231400-42242400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr15:42231600-42250000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr15:42232200-42240800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:42232200-42241000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:42232200-42244800	Genic enhancers	Fetal Muscle Leg	muscle
22	chr15:42232600-42239600	Strong transcription	Primary T cells from cord blood	blood
23	chr15:42233200-42244200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:42233600-42240200	Enhancers	Right Atrium	heart
25	chr15:42233600-42243000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr15:42233800-42239600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:42233800-42239800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:42234000-42239600	Genic enhancers	Lung	lung
29	chr15:42234000-42239800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr15:42234200-42241800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:42234400-42244000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr15:42235000-42242200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr15:42235000-42242400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr15:42235200-42239800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:42235400-42242000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:42235400-42242000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr15:42235400-42242000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr15:42235400-42244200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:42235600-42241400	Enhancers	Left Ventricle	heart
40	chr15:42235600-42242600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr15:42235800-42242000	Weak transcription	Liver	Liver
42	chr15:42236200-42242000	Enhancers	Fetal Muscle Trunk	muscle
43	chr15:42236600-42241800	Weak transcription	Fetal Lung	lung
44	chr15:42236600-42242000	Weak transcription	Ovary	ovary
45	chr15:42236800-42239600	Strong transcription	Spleen	Spleen
46	chr15:42236800-42239800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr15:42237000-42240200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:42237000-42242000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr15:42237000-42242600	Weak transcription	Colon Smooth Muscle	Colon
50	chr15:42237000-42242600	Weak transcription	Fetal Kidney	kidney

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