Variant report

Variant	rs6546030
Chromosome Location	chr2:64071651-64071652
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	POLR2A	chr2:64066467-64077414	H1-hESC	embryonic stem cell:	n/a	n/a
2	CHD1	chr2:64067067-64074747	H1-hESC	embryonic stem cell:	n/a	chr2:64068850-64068860 chr2:64068822-64068832 chr2:64068878-64068888 chr2:64067996-64068006
3	POLR2A	chr2:64071599-64071812	H1-hESC	embryonic stem cell:	n/a	n/a
4	SIN3A	chr2:64067165-64073428	H1-hESC	embryonic stem cell:	n/a	chr2:64073388-64073396
5	POLR2A	chr2:64071512-64072634	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr2:64071548-64072214	H1-hESC	embryonic stem cell:	n/a	n/a
7	TAF7	chr2:64067139-64075620	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64066407..64070482-chr2:64071096..64075382,10	MCF-7	breast:
2	chr2:64070153..64071712-chr2:64106669..64108533,2	K562	blood:

Variant related genes	Relation type
UGP2	TF binding region
ENSG00000169764	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10183479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10865344	0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs11558741	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11674020	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676710	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11683408	0.90[ASN][1000 genomes]
rs11686956	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11691987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693906	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11694253	0.82[ASN][1000 genomes]
rs11695421	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713498	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12991311	0.84[YRI][hapmap]
rs12996866	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13006124	0.84[YRI][hapmap]
rs13018690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13431781	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1440002	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17562177	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17562423	0.88[ASN][1000 genomes]
rs17619753	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs193031	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2302808	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2969395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs329478	0.90[ASN][1000 genomes]
rs329488	0.82[ASN][1000 genomes]
rs34122334	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34765999	0.90[ASN][1000 genomes]
rs34777730	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs35002211	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35336851	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35474183	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35480874	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35697586	0.90[ASN][1000 genomes]
rs35960986	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36033991	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36123537	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4233930	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4538187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4671073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs56904032	0.90[ASN][1000 genomes]
rs6546029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546031	0.91[AFR][1000 genomes]
rs6546032	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546033	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6546035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66980330	0.98[ASN][1000 genomes]
rs6710230	0.91[YRI][hapmap]
rs6710763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6715992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6726257	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs67308158	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6731508	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6732746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6755646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67615384	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67765474	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68117986	0.90[ASN][1000 genomes]
rs72808243	0.98[ASN][1000 genomes]
rs72893103	0.90[ASN][1000 genomes]
rs74181291	0.80[ASN][1000 genomes]
rs7590399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7597935	0.91[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64067000-64073200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr2:64067000-64075800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr2:64067000-64076400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:64067200-64071800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:64067200-64072000	Active TSS	Aorta	Aorta
6	chr2:64067200-64072000	Active TSS	Fetal Muscle Trunk	muscle
7	chr2:64067200-64072200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:64067200-64072200	Active TSS	Colonic Mucosa	Colon
9	chr2:64067200-64072400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:64067200-64073200	Active TSS	Left Ventricle	heart
11	chr2:64067200-64073400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:64067400-64072200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:64067400-64074000	Active TSS	H9 Cell Line	embryonic stem cell
14	chr2:64067600-64072800	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr2:64067600-64074000	Active TSS	Right Ventricle	heart
16	chr2:64067800-64071800	Active TSS	Fetal Muscle Leg	muscle
17	chr2:64069000-64071800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:64069000-64072800	Weak transcription	Spleen	Spleen
19	chr2:64069400-64072000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr2:64069400-64072000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:64069400-64072600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:64069400-64073400	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr2:64069400-64074600	Transcr. at gene 5' and 3'	Dnd41	blood
24	chr2:64069800-64073200	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
25	chr2:64070000-64072200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:64070000-64073600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:64070000-64082800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:64070200-64072200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr2:64070200-64072600	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr2:64070200-64076400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:64070200-64084600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:64070200-64103000	Weak transcription	Gastric	stomach
33	chr2:64070400-64071800	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr2:64070400-64071800	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr2:64070400-64072400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr2:64070400-64075800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:64070600-64071800	Enhancers	Duodenum Mucosa	Duodenum
38	chr2:64070600-64072000	Enhancers	K562	blood
39	chr2:64070600-64072000	Flanking Active TSS	NHEK	skin
40	chr2:64070600-64072600	Enhancers	Primary T cells from cord blood	blood
41	chr2:64070600-64073000	Enhancers	Brain Anterior Caudate	brain
42	chr2:64070600-64073000	Active TSS	GM12878-XiMat	blood
43	chr2:64070600-64073400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr2:64070600-64073400	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr2:64070600-64073800	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr2:64070600-64074400	Weak transcription	A549	lung
47	chr2:64070600-64076600	Enhancers	Brain Substantia Nigra	brain
48	chr2:64070600-64082800	Weak transcription	Fetal Stomach	stomach
49	chr2:64070600-64083800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:64070800-64071800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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