Variant report

Variant	rs1635
Chromosome Location	chr6:28227604-28227605
allele	G/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	ELF1	chr6:28226888-28227607	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:28219997..28223882-chr6:28224379..28228192,5	K562	blood:
2	chr6:28226019..28228390-chr6:28303494..28305290,2	K562	blood:
3	chr6:28218888..28222826-chr6:28224722..28227606,3	K562	blood:
4	chr6:28217539..28222258-chr6:28227412..28230016,4	MCF-7	breast:

Variant related genes	Relation type
ZKSCAN4	TF binding region
ENSG00000187626	Chromatin interaction
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10484542	0.85[CEU][hapmap]
rs12000	0.80[CHB][hapmap]
rs1233710	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1416919	0.85[CEU][hapmap]
rs16893827	0.85[CEU][hapmap]
rs16893917	0.85[CEU][hapmap]
rs16893973	0.85[CEU][hapmap]
rs16893975	0.85[CEU][hapmap]
rs17720687	0.82[CEU][hapmap]
rs2159275	0.85[CEU][hapmap]
rs2299030	1.00[CEU][hapmap]
rs3800327	0.85[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4711167	0.85[CEU][hapmap]
rs4713159	0.85[CEU][hapmap]
rs723475	0.85[CEU][hapmap]
rs723476	0.85[CEU][hapmap]
rs742107	0.85[CEU][hapmap]
rs758398	0.95[JPT][hapmap]
rs7750106	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757215	0.85[CEU][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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	22037552	GWAS catalog

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28225800-28227800	Active TSS	Colon Smooth Muscle	Colon
2	chr6:28226200-28228200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
3	chr6:28226400-28227800	Active TSS	Brain Anterior Caudate	brain
4	chr6:28226600-28227800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:28226600-28228400	Active TSS	Psoas Muscle	Psoas
6	chr6:28226800-28227800	Bivalent/Poised TSS	Fetal Kidney	kidney
7	chr6:28227000-28228400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:28227000-28232000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:28227000-28233800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:28227200-28227800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
11	chr6:28227200-28228200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr6:28227400-28227800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:28227400-28227800	Active TSS	Right Atrium	heart
14	chr6:28227400-28234400	Weak transcription	HSMMtube	muscle
15	chr6:28227600-28227800	Enhancers	Adipose Nuclei	Adipose
16	chr6:28227600-28227800	Weak transcription	HSMM	muscle
17	chr6:28227600-28228000	Weak transcription	Left Ventricle	heart
18	chr6:28227600-28228000	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr6:28227600-28228200	Active TSS	Right Ventricle	heart
20	chr6:28227600-28228400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:28227600-28229800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:28227600-28231600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:28227600-28231600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr6:28227600-28233600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:28227600-28233800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr6:28227600-28233800	Weak transcription	HMEC	breast

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