Variant report

Variant	rs13095392
Chromosome Location	chr3:24008040-24008041
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23985448..23989072-chr3:24007486..24009929,3	K562	blood:
2	chr3:23957307..23959478-chr3:24007546..24009448,2	MCF-7	breast:
3	chr3:23984107..23986878-chr3:24007871..24010163,2	MCF-7	breast:
4	chr3:23985888..23987972-chr3:24006975..24009368,2	K562	blood:

Variant related genes	Relation type
ENSG00000174738	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11717862	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13091509	0.85[EUR][1000 genomes]
rs4131403	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4241514	0.82[EUR][1000 genomes]
rs4241517	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[EUR][1000 genomes]
rs4241520	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4321479	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4589882	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4619734	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858094	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs4858095	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858098	0.92[CEU][hapmap];0.96[CHB][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858551	0.80[EUR][1000 genomes]
rs4858553	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs4858565	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858567	0.96[CEU][hapmap];0.95[CHB][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858569	0.83[CHB][hapmap]
rs5023610	0.92[CEU][hapmap];0.96[CHB][hapmap]
rs62253379	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6419846	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6550815	0.91[EUR][1000 genomes]
rs6550819	0.89[EUR][1000 genomes]
rs6550823	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6550824	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6550828	0.86[JPT][hapmap]
rs6550829	0.86[CHB][hapmap]
rs6764154	0.80[EUR][1000 genomes]
rs6778783	0.84[EUR][1000 genomes]
rs6779476	0.92[CEU][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6790557	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793391	0.80[EUR][1000 genomes]
rs6794922	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7371944	0.92[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7431301	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7615255	0.83[CEU][hapmap]
rs7626431	0.81[CEU][hapmap]
rs7636810	0.91[CHB][hapmap]
rs9310725	0.83[EUR][1000 genomes]
rs9845287	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs9879378	0.82[EUR][1000 genomes]
rs9882735	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]

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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23989200-24018000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:23989200-24020600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:23989200-24033200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:23989800-24017800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:23992400-24017400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:23993600-24009400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:23993600-24017800	Weak transcription	Brain Germinal Matrix	brain
8	chr3:23994000-24022800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:23996000-24012600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:23996200-24009400	Weak transcription	Psoas Muscle	Psoas
11	chr3:23996200-24011200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:23996200-24021200	Weak transcription	Small Intestine	intestine
13	chr3:23997200-24012200	Strong transcription	Liver	Liver
14	chr3:23999200-24011600	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:23999800-24019600	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr3:24000000-24020400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr3:24000600-24012200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:24000800-24010400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:24000800-24019600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr3:24000800-24021800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:24001000-24011000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:24001400-24010200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:24001400-24012600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:24001600-24012000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:24002400-24008600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:24002400-24010200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr3:24002600-24017600	Weak transcription	Stomach Mucosa	stomach
28	chr3:24002600-24020200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr3:24002800-24009200	Strong transcription	Fetal Intestine Small	intestine
30	chr3:24003000-24012600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:24003200-24008200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr3:24003200-24010400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:24003200-24011600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:24003400-24008400	Strong transcription	Fetal Muscle Leg	muscle
35	chr3:24003600-24010400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr3:24004000-24013200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:24004000-24016400	Weak transcription	Lung	lung
38	chr3:24004000-24017800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:24004000-24017800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr3:24004000-24017800	Weak transcription	Spleen	Spleen
41	chr3:24004000-24018000	Weak transcription	Esophagus	oesophagus
42	chr3:24004000-24022600	Weak transcription	Aorta	Aorta
43	chr3:24004000-24022600	Weak transcription	Pancreas	Pancrea
44	chr3:24004000-24023400	Weak transcription	Gastric	stomach
45	chr3:24004000-24023800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr3:24004200-24011200	Weak transcription	HepG2	liver
47	chr3:24004200-24022600	Weak transcription	Right Ventricle	heart
48	chr3:24004400-24008200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:24004400-24009400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:24004600-24008400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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