Variant report

Variant	rs2024115
Chromosome Location	chr4:3104568-3104569
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	chr4:3075725..3079021-chr4:3101094..3105877,5	MCF-7	breast:
2	chr4:3103289..3106037-chr4:3106708..3108502,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197386	Chromatin interaction
ENSG00000251075	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs110501	0.81[CEU][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.81[TSI][hapmap]
rs16843804	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16843836	0.92[ASN][1000 genomes]
rs17780797	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2071655	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2071704	0.83[TSI][hapmap]
rs2285086	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2285087	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28867436	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs362306	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs362331	0.81[CEU][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.81[TSI][hapmap]
rs363064	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs363066	1.00[CHB][hapmap]
rs363096	1.00[CHB][hapmap];0.80[CHD][hapmap];0.80[JPT][hapmap]
rs3856973	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.88[ASN][1000 genomes]
rs3905238	0.80[EUR][1000 genomes]
rs4498089	0.86[ASN][1000 genomes]
rs4690071	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4690072	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4690073	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs55962025	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61348208	0.94[ASN][1000 genomes]
rs6446722	0.89[ASN][1000 genomes]
rs6446723	0.81[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6844859	0.81[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap]
rs6855981	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs73191188	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs762855	0.86[TSI][hapmap]
rs7659144	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7685686	0.81[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap]
rs7691627	0.84[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs82333	0.84[CEU][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.83[TSI][hapmap]
rs916171	0.84[CEU][hapmap];0.81[CHB][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.88[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription 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	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3078200-3109800	Weak transcription	Stomach Mucosa	stomach
2	chr4:3078400-3107000	Weak transcription	HMEC	breast
3	chr4:3078600-3113800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:3078800-3108800	Weak transcription	Psoas Muscle	Psoas
5	chr4:3079800-3107200	Weak transcription	Fetal Brain Male	brain
6	chr4:3080000-3117800	Weak transcription	Small Intestine	intestine
7	chr4:3084400-3109000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr4:3084600-3109000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:3085600-3107000	Weak transcription	K562	blood
10	chr4:3087800-3108800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:3088200-3164200	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr4:3092400-3108200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr4:3093400-3108800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr4:3093600-3109200	Weak transcription	Fetal Heart	heart
15	chr4:3094400-3123400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:3094600-3105000	Strong transcription	Primary B cells from cord blood	blood
17	chr4:3095000-3108200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr4:3095200-3109000	Weak transcription	A549	lung
19	chr4:3095600-3107200	Weak transcription	HSMMtube	muscle
20	chr4:3096400-3108000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:3097000-3108200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr4:3097200-3143400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:3097200-3162200	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:3097400-3107400	Strong transcription	GM12878-XiMat	blood
25	chr4:3097400-3107800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:3097400-3163800	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr4:3097600-3104600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:3098000-3162600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:3098600-3109800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr4:3099800-3108200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr4:3099800-3108200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr4:3099800-3114400	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:3100000-3104800	Strong transcription	Dnd41	blood
34	chr4:3100000-3107800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:3100000-3108000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:3100000-3108200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr4:3100000-3110400	Strong transcription	Primary hematopoietic stem cells	blood
38	chr4:3100000-3159400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr4:3100400-3104800	Strong transcription	Primary T cells from cord blood	blood
40	chr4:3100400-3112000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:3100600-3104800	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr4:3100600-3106400	Weak transcription	NHDF-Ad	bronchial
43	chr4:3100600-3108000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:3100600-3108400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr4:3100800-3104600	Strong transcription	Brain Cingulate Gyrus	brain
46	chr4:3100800-3104800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:3100800-3104800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:3100800-3104800	Strong transcription	Liver	Liver
49	chr4:3100800-3104800	Strong transcription	Brain Hippocampus Middle	brain
50	chr4:3100800-3104800	Strong transcription	Rectal Mucosa Donor 29	rectum

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