Variant report

Variant	rs68168863
Chromosome Location	chr6:33758238-33758239
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	CTCF	chr6:33758160-33758310	AG04449	skin:	n/a	n/a
2	TEAD4	chr6:33758048-33758489	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr6:33758055-33758412	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr6:33758120-33758270	AG10803	skin:	n/a	n/a
5	POLR2A	chr6:33758238-33758469	IMR90	lung:	n/a	n/a
6	POLR2A	chr6:33754903-33758533	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33677680..33679812-chr6:33755384..33758328,2	MCF-7	breast:
2	chr6:33677771..33685795-chr6:33753004..33758704,10	MCF-7	breast:
3	chr6:33756927..33758602-chr6:33764987..33767346,2	MCF-7	breast:

Variant related genes	Relation type
LEMD2	TF binding region
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10456075	0.82[ASN][1000 genomes]
rs10456420	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10456421	0.93[EUR][1000 genomes]
rs10947418	0.86[AFR][1000 genomes]
rs10947432	0.82[ASN][1000 genomes]
rs11755257	0.86[AFR][1000 genomes]
rs11757612	0.86[AFR][1000 genomes]
rs11758330	0.86[AFR][1000 genomes]
rs12153877	0.98[EUR][1000 genomes]
rs12189725	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12192035	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12192087	0.92[EUR][1000 genomes]
rs12193658	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12195409	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12198383	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12199132	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12200154	0.86[AFR][1000 genomes]
rs12203688	0.88[ASN][1000 genomes]
rs12204620	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12204992	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12205398	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12211490	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211554	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211565	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215329	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661400	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12662447	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13200063	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13204162	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13206228	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207666	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13213889	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13214874	0.82[ASN][1000 genomes]
rs2274459	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281831	0.88[ASN][1000 genomes]
rs2296749	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34139049	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34339105	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34460651	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs34472165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34869648	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34884883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35274562	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35328423	0.88[EUR][1000 genomes]
rs35366046	0.92[EUR][1000 genomes]
rs35445446	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35646598	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35698850	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35721478	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35797388	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35964955	0.83[EUR][1000 genomes]
rs36122085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3793080	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3806107	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66617522	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs66670017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925337	0.94[EUR][1000 genomes]
rs71565393	0.86[AFR][1000 genomes]
rs729376	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs751095	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs755239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877187	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	esv3436027	chr6:33754374-33758772	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33757000-33758800	Enhancers	Spleen	Spleen
2	chr6:33757000-33760000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:33757000-33760200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:33757200-33759600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:33757200-33760000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:33757400-33759000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:33757400-33759400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:33757400-33759400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr6:33757400-33761400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr6:33757600-33758600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:33757600-33758800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr6:33757600-33758800	Weak transcription	Gastric	stomach
13	chr6:33757600-33758800	Enhancers	Osteobl	bone
14	chr6:33757600-33759000	Enhancers	H9 Cell Line	embryonic stem cell
15	chr6:33757600-33759000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:33757600-33759200	Weak transcription	Thymus	Thymus
17	chr6:33757600-33759400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:33757600-33759400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:33757600-33759800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr6:33757600-33759800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr6:33757600-33760200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:33757600-33760800	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr6:33757600-33761000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:33757600-33762400	Weak transcription	A549	lung
25	chr6:33757600-33763600	Enhancers	H1 Cell Line	embryonic stem cell
26	chr6:33757600-33775800	Weak transcription	Right Atrium	heart
27	chr6:33757800-33758400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:33757800-33758800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:33757800-33759000	Enhancers	HSMMtube	muscle
30	chr6:33757800-33759200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:33757800-33759200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:33758000-33758400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr6:33758000-33758800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:33758000-33758800	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr6:33758000-33760000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:33758000-33762400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:33758200-33758400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr6:33758200-33758600	Weak transcription	HSMM	muscle
39	chr6:33758200-33759400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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