Variant report

Variant	rs17093639
Chromosome Location	chr12:44132928-44132929
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	chr12:44128669..44131502-chr12:44132445..44134244,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IRAK4-2	chr12:44132824-44133167	NONHSAT027803
2	lnc-IRAK4-2	chr12:44132824-44132992	NONHSAT027802

Variant related genes	Relation type
ENSG00000257896	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1057190	0.89[MEX][hapmap]
rs10880565	0.89[MEX][hapmap]
rs11182240	0.89[MEX][hapmap]
rs12302873	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12305949	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12312327	1.00[MEX][hapmap]
rs12315211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12318086	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap]
rs12319024	0.89[MEX][hapmap]
rs4251429	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs4251447	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs4251481	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs4251488	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs4251522	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs4251527	0.82[JPT][hapmap]
rs57291280	0.83[AFR][1000 genomes]
rs7954870	1.00[ASN][1000 genomes]
rs7956245	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7979691	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9783418	0.89[MEX][hapmap]
rs9971859	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap]
rs9971895	0.82[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][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	nsv558750	chr12:44002268-44132928	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv933142	chr12:44130156-44278300	Active TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44117000-44138000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr12:44117400-44151400	Weak transcription	Brain Substantia Nigra	brain
3	chr12:44117800-44136000	Weak transcription	A549	lung
4	chr12:44117800-44144600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:44119400-44146000	Weak transcription	Aorta	Aorta
6	chr12:44119800-44138200	Weak transcription	Fetal Lung	lung
7	chr12:44119800-44146000	Weak transcription	Fetal Brain Female	brain
8	chr12:44119800-44147000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:44120000-44151600	Weak transcription	Gastric	stomach
10	chr12:44120200-44151600	Weak transcription	Lung	lung
11	chr12:44122000-44147400	Weak transcription	Psoas Muscle	Psoas
12	chr12:44122600-44139800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr12:44122600-44147400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:44122600-44152000	Weak transcription	Left Ventricle	heart
15	chr12:44122800-44135800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:44122800-44138600	Weak transcription	Brain Germinal Matrix	brain
17	chr12:44122800-44151000	Weak transcription	Fetal Brain Male	brain
18	chr12:44123400-44151600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:44123600-44151400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:44124800-44136800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:44125000-44151400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:44125000-44151400	Weak transcription	HUVEC	blood vessel
23	chr12:44125200-44138400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:44125800-44134400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:44126000-44139400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr12:44126200-44145800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:44126200-44150400	Weak transcription	Small Intestine	intestine
28	chr12:44126400-44137200	Strong transcription	K562	blood
29	chr12:44126400-44146000	Weak transcription	Esophagus	oesophagus
30	chr12:44126400-44151600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:44126400-44151600	Weak transcription	Colonic Mucosa	Colon
32	chr12:44126400-44151600	Weak transcription	Right Ventricle	heart
33	chr12:44126600-44147200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr12:44127200-44151600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:44127600-44133400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:44127600-44141200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:44128000-44135200	Weak transcription	Fetal Heart	heart
38	chr12:44128400-44139000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:44128600-44151600	Weak transcription	Spleen	Spleen
40	chr12:44128800-44151400	Weak transcription	Brain Angular Gyrus	brain
41	chr12:44129200-44133400	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr12:44129800-44134600	Weak transcription	HSMMtube	muscle
43	chr12:44130400-44134200	Weak transcription	HepG2	liver
44	chr12:44130400-44134400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:44130400-44136800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:44130400-44146200	Weak transcription	Brain Hippocampus Middle	brain
47	chr12:44130400-44150200	Weak transcription	Stomach Mucosa	stomach
48	chr12:44130600-44133000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:44130600-44133200	Weak transcription	Fetal Intestine Small	intestine
50	chr12:44130600-44133200	Weak transcription	Fetal Stomach	stomach

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