Variant report

Variant	rs1547668
Chromosome Location	chr6:33775446-33775447
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33774712..33778330-chr6:33783087..33786924,3	K562	blood:
2	chr6:33759898..33762472-chr6:33773491..33776525,3	K562	blood:
3	chr6:33773235..33775828-chr6:33782693..33785367,2	K562	blood:
4	chr6:33770966..33772879-chr6:33773435..33775857,2	K562	blood:

Variant related genes	Relation type
ENSG00000096395	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10947428	0.84[CEU][hapmap]
rs10947436	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10947446	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11751943	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1536500	0.83[EUR][1000 genomes]
rs1536501	0.84[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1951930	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1998949	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs2182658	0.84[YRI][hapmap]
rs2182659	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2395399	0.84[ASW][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs2395401	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2395447	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2395448	0.89[CEU][hapmap]
rs3957165	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs3998115	1.00[JPT][hapmap]
rs4711350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4713685	0.84[LWK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs4713687	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4713688	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs487835	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4996879	0.84[EUR][1000 genomes]
rs530614	0.84[ASW][hapmap];0.89[CEU][hapmap];0.80[LWK][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs570749	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs602399	0.84[ASW][hapmap];0.89[CEU][hapmap];0.83[LWK][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs652049	0.84[ASW][hapmap];0.89[CEU][hapmap];0.80[LWK][hapmap];0.81[MEX][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs688209	0.84[CEU][hapmap]
rs6915136	1.00[JPT][hapmap]
rs751727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs756138	0.81[YRI][hapmap]
rs756139	0.81[YRI][hapmap]
rs7739273	0.83[YRI][hapmap]
rs942496	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs943463	0.89[CEU][hapmap]
rs943464	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs943472	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs943476	0.83[ASW][hapmap];0.84[YRI][hapmap]
rs9461905	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs9461907	0.83[EUR][1000 genomes]

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	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
2	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1547668	LEMD2	cis	Thyroid	GTEx
rs1547668	C6orf125	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33757600-33775800	Weak transcription	Right Atrium	heart
2	chr6:33766000-33776000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:33766800-33776400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:33770400-33776000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:33770600-33776200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:33771000-33776200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:33771400-33777000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:33772400-33775800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:33772400-33776200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:33772800-33775600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:33773200-33777400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:33773200-33777400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:33774400-33777600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:33774600-33776200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:33774800-33775800	Enhancers	Brain Germinal Matrix	brain
16	chr6:33774800-33775800	Enhancers	Fetal Muscle Leg	muscle
17	chr6:33774800-33776200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr6:33774800-33776400	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr6:33774800-33776400	Bivalent Enhancer	Adipose Nuclei	Adipose
20	chr6:33775000-33775800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:33775000-33776200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
22	chr6:33775000-33776400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
23	chr6:33775000-33776400	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr6:33775000-33776400	Enhancers	Left Ventricle	heart
25	chr6:33775000-33776400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
26	chr6:33775000-33776600	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr6:33775000-33777000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:33775200-33775600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr6:33775200-33775600	Enhancers	GM12878-XiMat	blood
30	chr6:33775200-33775800	Enhancers	Primary B cells from cord blood	blood
31	chr6:33775200-33776000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
32	chr6:33775200-33776000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:33775200-33776000	Enhancers	Spleen	Spleen
34	chr6:33775200-33776000	Bivalent Enhancer	HUVEC	blood vessel
35	chr6:33775200-33776200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr6:33775200-33776400	Bivalent Enhancer	Primary T cells from cord blood	blood
37	chr6:33775200-33776400	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr6:33775200-33776400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr6:33775200-33776400	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:33775200-33776800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:33775200-33777200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
42	chr6:33775400-33775600	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr6:33775400-33775800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
44	chr6:33775400-33775800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
45	chr6:33775400-33775800	Bivalent Enhancer	Fetal Thymus	thymus
46	chr6:33775400-33775800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
47	chr6:33775400-33776000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:33775400-33776000	Bivalent Enhancer	Dnd41	blood
49	chr6:33775400-33776200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
50	chr6:33775400-33776200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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