Variant report

Variant	rs9790069
Chromosome Location	chr3:141460532-141460533
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141459822..141461407-chr3:141463215..141465670,2	MCF-7	breast:
2	chr3:141458745..141461557-chr3:141613414..141615464,2	K562	blood:
3	chr3:141455466..141460652-chr3:141593125..141598625,15	K562	blood:
4	chr3:141459507..141461128-chr3:141567527..141569442,2	K562	blood:
5	chr3:141460404..141464291-chr3:141593804..141597029,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114125	Chromatin interaction
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12487528	1.00[ASW][hapmap]
rs16851692	1.00[EUR][1000 genomes]
rs16851717	1.00[CHB][hapmap]
rs16851740	1.00[CHB][hapmap]
rs16851763	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1879286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34769632	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3773840	1.00[CHB][hapmap]
rs4538350	1.00[CHB][hapmap]
rs55712018	1.00[AFR][1000 genomes]
rs59077856	1.00[EUR][1000 genomes]
rs59379866	1.00[EUR][1000 genomes]
rs59538463	1.00[EUR][1000 genomes]
rs7632069	1.00[CHB][hapmap]
rs9790073	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer 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 target site	61 gene(s)	inside rSNPs	diseases
2	nsv877552	chr3:141420562-141466147	Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141458000-141461400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:141458200-141461000	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr3:141458200-141470400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:141458400-141460600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:141458400-141463600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:141458400-141464000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:141458600-141461400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr3:141458600-141463200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:141458600-141468000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:141458800-141460800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr3:141458800-141461400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:141458800-141461400	Weak transcription	Right Ventricle	heart
13	chr3:141458800-141461600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:141458800-141470800	Weak transcription	Stomach Mucosa	stomach
15	chr3:141459000-141460600	Enhancers	Brain Germinal Matrix	brain
16	chr3:141459000-141460600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:141459000-141461000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:141459000-141461200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:141459000-141461400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:141459000-141461400	Weak transcription	Placenta	Placenta
21	chr3:141459000-141462000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:141459000-141462400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:141459000-141463200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr3:141459000-141463400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:141459000-141463600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:141459000-141463600	Weak transcription	Esophagus	oesophagus
27	chr3:141459000-141465600	Weak transcription	Lung	lung
28	chr3:141459000-141465800	Weak transcription	Gastric	stomach
29	chr3:141459200-141460600	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr3:141459200-141460600	Genic enhancers	HSMM	muscle
31	chr3:141459200-141461400	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr3:141459400-141461400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:141459400-141464000	Weak transcription	Fetal Stomach	stomach
34	chr3:141459600-141460600	Enhancers	Primary hematopoietic stem cells	blood
35	chr3:141459600-141460600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr3:141459600-141460600	Enhancers	A549	lung
37	chr3:141459600-141461400	Enhancers	Pancreas	Pancrea
38	chr3:141459600-141463400	Weak transcription	Fetal Brain Female	brain
39	chr3:141459600-141464200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:141459600-141470800	Weak transcription	Fetal Brain Male	brain
41	chr3:141459800-141460600	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr3:141459800-141460600	Genic enhancers	HUVEC	blood vessel
43	chr3:141459800-141460600	Genic enhancers	NH-A	brain
44	chr3:141459800-141460800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:141459800-141461000	Genic enhancers	Fetal Thymus	thymus
46	chr3:141459800-141463400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr3:141460000-141460800	Weak transcription	Brain Substantia Nigra	brain
48	chr3:141460000-141461200	Enhancers	Colon Smooth Muscle	Colon
49	chr3:141460000-141463600	Weak transcription	Fetal Kidney	kidney
50	chr3:141460000-141467000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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