Variant report

Variant	rs12639929
Chromosome Location	chr4:174156538-174156539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:174155629..174158064-chr4:174160464..174162716,2	K562	blood:
2	chr4:174089806..174092748-chr4:174153971..174156651,2	MCF-7	breast:
3	chr4:174155629..174158011-chr4:174160464..174162573,2	K562	blood:

Variant related genes	Relation type
ENSG00000109586	Chromatin interaction
ENSG00000245213	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10011724	0.86[EUR][1000 genomes]
rs10027708	0.84[EUR][1000 genomes]
rs10031414	0.86[EUR][1000 genomes]
rs1054496	0.86[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs1054497	0.86[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs11737748	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12503879	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12503939	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12644699	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13111572	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13112928	0.87[CHB][hapmap]
rs13125240	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13138282	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1574314	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs17322893	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1991727	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs2078475	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2332654	0.86[EUR][1000 genomes]
rs2332668	0.87[EUR][1000 genomes]
rs2332669	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs28477433	0.86[EUR][1000 genomes]
rs28612521	0.86[EUR][1000 genomes]
rs28709762	0.83[EUR][1000 genomes]
rs2877748	0.91[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs3733477	0.88[EUR][1000 genomes]
rs4377567	0.82[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs4419455	0.82[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs4561909	0.91[ASW][hapmap];0.86[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4643788	0.84[EUR][1000 genomes]
rs4695826	0.85[EUR][1000 genomes]
rs6814857	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs6826412	0.88[EUR][1000 genomes]
rs6835098	0.86[EUR][1000 genomes]
rs6851632	0.88[EUR][1000 genomes]
rs7671278	0.85[EUR][1000 genomes]
rs7672108	1.00[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs9990666	0.84[EUR][1000 genomes]
rs9997477	0.91[CEU][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799519	chr4:174090004-174173743	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv3468078	chr4:174149437-174156708	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv3468079	chr4:174149437-174156708	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174104000-174157200	Weak transcription	Ovary	ovary
2	chr4:174114200-174157800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:174123600-174174200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr4:174126600-174163400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr4:174127000-174163600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr4:174127000-174163600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr4:174128200-174169200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr4:174131800-174168600	Weak transcription	Gastric	stomach
9	chr4:174136600-174158400	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:174136800-174157200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:174139000-174157600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:174140400-174158200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:174140400-174163400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr4:174140400-174163600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:174140400-174163600	Weak transcription	Aorta	Aorta
16	chr4:174140600-174158000	Weak transcription	Hela-S3	cervix
17	chr4:174140600-174158200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:174140600-174158600	Weak transcription	HSMMtube	muscle
19	chr4:174142200-174173400	Weak transcription	Lung	lung
20	chr4:174144200-174169000	Weak transcription	Fetal Intestine Large	intestine
21	chr4:174145800-174163800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:174145800-174163800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr4:174148000-174157200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:174148000-174157400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr4:174148000-174173400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:174148600-174157200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:174149200-174157000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:174150200-174163800	Weak transcription	Psoas Muscle	Psoas
29	chr4:174150200-174173400	Weak transcription	Small Intestine	intestine
30	chr4:174150400-174157800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:174151200-174158200	Weak transcription	A549	lung
32	chr4:174151200-174163200	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr4:174151400-174157000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr4:174151400-174163000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:174151400-174171000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr4:174152600-174160600	Weak transcription	Fetal Brain Male	brain
37	chr4:174152600-174173400	Weak transcription	Left Ventricle	heart
38	chr4:174152800-174158200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr4:174153000-174169200	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr4:174153600-174171000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr4:174153800-174156600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr4:174153800-174162800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:174154000-174156800	Strong transcription	Primary T cells from cord blood	blood
44	chr4:174154000-174157600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:174154200-174157200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:174154200-174157600	Weak transcription	Colonic Mucosa	Colon
47	chr4:174154400-174163200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr4:174154600-174157200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:174154800-174159200	Enhancers	Fetal Lung	lung
50	chr4:174155000-174156800	Strong transcription	Primary B cells from cord blood	blood

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