Variant report

Variant	rs6744629
Chromosome Location	chr2:189160338-189160339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr2:189159929-189160342	MCF10A-Er-Src	breast:	n/a	n/a
2	CHD1	chr2:189156501-189161129	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr2:189155279-189161412	SK-N-SH	brain:	n/a	n/a
4	FOS	chr2:189160040-189160380	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr2:189160042-189160362	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr2:189160131-189160368	HepG2	liver:	n/a	chr2:189160230-189160241

No.	Distal block	Cell Line	Cell type
1	chr2:189159403..189162059-chr2:189193708..189195307,2	K562	blood:
2	chr2:189155055..189158409-chr2:189159948..189163832,8	K562	blood:
3	chr2:189156064..189158162-chr2:189159992..189162914,5	K562	blood:
4	chr2:189148121..189153367-chr2:189154784..189162424,9	K562	blood:
5	chr2:189159168..189161448-chr2:189298953..189301170,2	MCF-7	breast:

Variant related genes	Relation type
MIR561	TF binding region
ENSG00000231689	Chromatin interaction
ENSG00000144366	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10174928	0.81[JPT][hapmap]
rs10175259	0.88[ASN][1000 genomes]
rs10180222	0.93[ASN][1000 genomes]
rs10193506	0.82[CEU][hapmap]
rs10197499	0.80[EUR][1000 genomes]
rs1036649	0.80[ASN][1000 genomes]
rs10804020	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10931343	0.82[ASN][1000 genomes]
rs10931344	0.82[ASN][1000 genomes]
rs10931346	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10931355	0.81[JPT][hapmap]
rs10931356	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10931359	0.96[CEU][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11900558	0.82[ASN][1000 genomes]
rs12329399	0.81[JPT][hapmap]
rs12464904	0.82[ASN][1000 genomes]
rs12465164	0.96[CEU][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12465625	1.00[CEU][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.85[EUR][1000 genomes]
rs12469904	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12473653	0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs12474692	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12611919	0.89[CEU][hapmap]
rs12613615	0.92[ASN][1000 genomes]
rs12619361	0.93[ASN][1000 genomes]
rs12624002	0.93[CEU][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12693487	0.82[ASN][1000 genomes]
rs12693489	0.92[ASN][1000 genomes]
rs12987194	0.81[JPT][hapmap]
rs13008931	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13014693	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13022513	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13389155	0.81[JPT][hapmap]
rs13424536	0.81[JPT][hapmap]
rs1898986	0.80[ASN][1000 genomes]
rs34189381	0.85[ASN][1000 genomes]
rs34445909	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35365782	0.82[EUR][1000 genomes]
rs35964306	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4274570	0.80[JPT][hapmap]
rs4294965	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4361092	0.81[JPT][hapmap]
rs4381753	0.86[EUR][1000 genomes]
rs4396679	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4398237	0.81[JPT][hapmap]
rs4402719	0.94[ASN][1000 genomes]
rs4402720	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4413123	0.83[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4426503	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4430902	0.81[JPT][hapmap]
rs4433962	0.81[JPT][hapmap]
rs4500907	0.82[ASN][1000 genomes]
rs4513258	0.81[JPT][hapmap]
rs4516391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4522565	0.81[JPT][hapmap]
rs4564741	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4591312	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4599076	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4610010	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4640356	0.81[JPT][hapmap]
rs4641903	0.82[ASN][1000 genomes]
rs4666758	0.81[JPT][hapmap]
rs4666759	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4667215	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4667221	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4667222	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs4992744	0.81[JPT][hapmap]
rs59106803	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62183206	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62183212	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62183213	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6434269	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6711822	0.85[ASN][1000 genomes]
rs6712056	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6719273	0.82[ASN][1000 genomes]
rs67211370	0.85[ASN][1000 genomes]
rs67240894	0.80[ASN][1000 genomes]
rs6724636	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6724867	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6729182	0.81[JPT][hapmap]
rs6739162	0.81[JPT][hapmap]
rs6744150	0.82[ASN][1000 genomes]
rs6753371	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7420700	0.81[JPT][hapmap]
rs7425596	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7566619	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7574262	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7585703	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[ASN][1000 genomes]
rs7586390	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7593215	0.81[JPT][hapmap]
rs7593546	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7598279	0.95[ASN][1000 genomes]
rs7598785	0.82[ASN][1000 genomes]
rs7599516	0.94[ASN][1000 genomes]
rs7606178	0.80[YRI][hapmap]
rs893745	0.85[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap]

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	nsv1010394	chr2:188994398-189284092	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv998395	chr2:189018246-189284092	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189155200-189161800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:189155400-189160800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:189155400-189161000	Active TSS	Aorta	Aorta
4	chr2:189155400-189161200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:189155400-189161200	Active TSS	K562	blood
6	chr2:189155400-189161600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr2:189155600-189161200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr2:189155600-189161600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:189155600-189161800	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr2:189155800-189161200	Active TSS	Placenta	Placenta
11	chr2:189155800-189161200	Active TSS	A549	lung
12	chr2:189155800-189161400	Active TSS	H1 Cell Line	embryonic stem cell
13	chr2:189156000-189161000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:189156000-189161200	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr2:189156000-189161600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:189156200-189160800	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr2:189156400-189160400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:189158000-189163600	Weak transcription	Lung	lung
19	chr2:189158200-189161400	Flanking Active TSS	HUVEC	blood vessel
20	chr2:189158400-189160800	Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr2:189158800-189160400	Flanking Active TSS	Fetal Lung	lung
22	chr2:189159000-189160400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:189159000-189161600	Active TSS	Fetal Brain Female	brain
24	chr2:189159000-189163600	Weak transcription	Pancreas	Pancrea
25	chr2:189159000-189168000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:189159000-189168000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:189159200-189160800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:189159200-189161000	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:189159200-189163400	Weak transcription	Stomach Mucosa	stomach
30	chr2:189159200-189168000	Weak transcription	Psoas Muscle	Psoas
31	chr2:189159200-189171200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:189159400-189160800	Weak transcription	Brain Germinal Matrix	brain
33	chr2:189159600-189161000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:189159800-189160400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:189159800-189160800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:189160000-189160400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:189160000-189160400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr2:189160000-189161000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:189160000-189172800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:189160200-189160400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:189160200-189160400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr2:189160200-189160400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:189160200-189160400	Flanking Active TSS	Fetal Intestine Large	intestine
44	chr2:189160200-189160400	Enhancers	NH-A	brain
45	chr2:189160200-189160400	Enhancers	NHLF	lung
46	chr2:189160200-189160800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:189160200-189160800	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr2:189160200-189161000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:189160200-189161000	Weak transcription	Fetal Kidney	kidney
50	chr2:189160200-189161200	Enhancers	Fetal Intestine Small	intestine

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