Variant report

Variant	rs6704769
Chromosome Location	chr2:54769290-54769291
allele	A/G
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	RUNX3	chr2:54769159-54769508	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:54767808..54771330-chr2:54771769..54776449,4	K562	blood:
2	chr2:54764232..54766337-chr2:54769153..54772806,3	K562	blood:
3	chr2:54764431..54771229-chr2:54784220..54787609,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228108	TF binding region
ENSG00000115306	Chromatin interaction
ENSG00000234943	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10165490	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10180713	0.82[EUR][1000 genomes]
rs1047499	0.82[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs11892788	0.82[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs11898012	0.80[CHB][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs12104998	0.91[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12105792	0.91[CEU][hapmap];0.80[CHB][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12467581	0.84[EUR][1000 genomes]
rs12468469	0.85[EUR][1000 genomes]
rs12617036	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12713260	0.85[EUR][1000 genomes]
rs13016942	0.95[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13399435	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs1367295	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1541854	0.85[EUR][1000 genomes]
rs17344044	0.80[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs17344072	0.95[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17521078	0.91[CEU][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs1802889	0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1864493	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2292356	0.81[EUR][1000 genomes]
rs2292357	0.83[EUR][1000 genomes]
rs2941586	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs2941587	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs2941595	0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs2971877	0.82[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs2971879	0.82[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2971887	0.81[EUR][1000 genomes]
rs3796014	0.82[EUR][1000 genomes]
rs4233952	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4233954	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4444573	0.84[EUR][1000 genomes]
rs4455199	0.86[EUR][1000 genomes]
rs4514917	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4514918	0.90[ASN][1000 genomes]
rs4519562	0.84[EUR][1000 genomes]
rs4592889	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4671221	0.90[CEU][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs4671222	0.91[CEU][hapmap];0.81[CHB][hapmap];0.90[EUR][1000 genomes]
rs4671225	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4671226	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4671945	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs4671946	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4671947	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4671949	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4671950	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671951	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.84[TSI][hapmap];0.93[EUR][1000 genomes]
rs4671954	0.85[EUR][1000 genomes]
rs4671955	0.88[EUR][1000 genomes]
rs4671956	0.95[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4671960	0.83[TSI][hapmap]
rs4671961	0.83[TSI][hapmap]
rs4990319	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56381959	0.81[ASN][1000 genomes]
rs6545411	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs6545413	0.86[EUR][1000 genomes]
rs6545414	0.86[EUR][1000 genomes]
rs6545415	0.95[CEU][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap];0.86[EUR][1000 genomes]
rs6545418	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6545419	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6545420	0.87[ASN][1000 genomes]
rs6545421	0.89[ASN][1000 genomes]
rs6545427	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6545429	0.95[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6545434	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs6706372	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs6724590	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6729826	0.95[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes]
rs6731661	0.84[EUR][1000 genomes]
rs6732949	0.84[EUR][1000 genomes]
rs6734658	0.85[EUR][1000 genomes]
rs6735813	0.83[EUR][1000 genomes]
rs6742607	0.84[EUR][1000 genomes]
rs6746016	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs6746306	0.89[EUR][1000 genomes]
rs6748816	0.84[EUR][1000 genomes]
rs6761369	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6761398	0.91[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7558950	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7563706	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7589236	0.95[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7607451	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs907135	0.97[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv528848	chr2:54758305-54777576	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
2	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
4	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
6	chr2:54750800-54769800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:54757000-54776800	Weak transcription	Brain Germinal Matrix	brain
9	chr2:54757400-54771000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr2:54758200-54778200	Weak transcription	Placenta	Placenta
11	chr2:54758600-54772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:54760400-54769600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:54761000-54769400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:54761600-54773200	Weak transcription	Fetal Brain Male	brain
15	chr2:54761800-54769600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:54762000-54775400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:54762200-54770400	Weak transcription	Fetal Kidney	kidney
18	chr2:54762200-54772800	Weak transcription	Aorta	Aorta
19	chr2:54762200-54772800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:54762200-54773800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:54762400-54770800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:54762400-54772600	Weak transcription	Liver	Liver
23	chr2:54762800-54772600	Weak transcription	NHDF-Ad	bronchial
24	chr2:54763000-54776000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr2:54763200-54770800	Weak transcription	Fetal Intestine Small	intestine
26	chr2:54763200-54772600	Weak transcription	NHLF	lung
27	chr2:54764000-54776800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:54764400-54772600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:54764600-54769400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:54764600-54772600	Weak transcription	Osteobl	bone
31	chr2:54764800-54769400	Weak transcription	Fetal Stomach	stomach
32	chr2:54764800-54769400	Weak transcription	Psoas Muscle	Psoas
33	chr2:54765600-54774000	Weak transcription	Fetal Brain Female	brain
34	chr2:54766000-54769600	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:54766200-54772800	Weak transcription	Small Intestine	intestine
36	chr2:54766600-54771000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:54767000-54770200	Enhancers	Fetal Heart	heart
38	chr2:54767200-54769400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:54767200-54770000	Weak transcription	Lung	lung
40	chr2:54767200-54771200	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr2:54767200-54771600	Enhancers	Brain Angular Gyrus	brain
42	chr2:54767200-54771600	Enhancers	Brain Hippocampus Middle	brain
43	chr2:54767400-54772600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:54767400-54772800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:54767600-54769800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr2:54767600-54770000	Enhancers	Brain Cingulate Gyrus	brain
47	chr2:54767800-54772600	Weak transcription	HUVEC	blood vessel
48	chr2:54767800-54772600	Weak transcription	NH-A	brain
49	chr2:54767800-54773000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:54768200-54769400	Weak transcription	Right Ventricle	heart

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