Variant report

Variant	rs29235
Chromosome Location	chr6:29624078-29624079
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	MEF2C	chr6:29623790-29624275	GM12878	blood:	n/a	chr6:29624052-29624066 chr6:29624054-29624065 chr6:29624052-29624067 chr6:29624050-29624071 chr6:29624050-29624071
2	SRF	chr6:29623915-29624088	GM12878	blood:	n/a	chr6:29624014-29624025 chr6:29624010-29624024 chr6:29624013-29624026 chr6:29624014-29624028 chr6:29624011-29624028 chr6:29624015-29624024 chr6:29624012-29624027 chr6:29624013-29624026 chr6:29624010-29624028
3	CTCF	chr6:29624040-29624190	GM12873	blood:	n/a	n/a
4	MEF2C	chr6:29623942-29624230	GM12878	blood:	n/a	chr6:29624052-29624066 chr6:29624054-29624065 chr6:29624052-29624067 chr6:29624050-29624071 chr6:29624050-29624071
5	MEF2A	chr6:29623892-29624272	GM12878	blood:	n/a	chr6:29624052-29624066 chr6:29624054-29624065 chr6:29624050-29624071 chr6:29624050-29624071
6	CTCF	chr6:29624040-29624190	HEK293	kidney:	n/a	n/a
7	MEF2A	chr6:29623809-29624302	GM12878	blood:	n/a	chr6:29624052-29624066 chr6:29624054-29624065 chr6:29624050-29624071 chr6:29624050-29624071

Variant related genes	Relation type
MOG	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17178518	0.86[ASN][1000 genomes]
rs17178532	0.86[ASN][1000 genomes]
rs2747420	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs29234	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29238	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs29240	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs29272	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3025623	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3909134	0.86[ASN][1000 genomes]
rs73747624	0.86[ASN][1000 genomes]
rs9461541	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468571	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468572	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9500947	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv527037	chr6:29615822-29624112	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs29235	HLA-A	cis	lymphoblastoid	seeQTL
rs29235	LOC347981	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29618400-29624600	Weak transcription	Right Atrium	heart
2	chr6:29618400-29629000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:29618400-29629600	Weak transcription	Right Ventricle	heart
4	chr6:29618600-29624600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:29620000-29628800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr6:29620000-29631200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:29620200-29624200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:29620600-29626600	Enhancers	Fetal Heart	heart
9	chr6:29621000-29625000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr6:29621800-29625000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr6:29622000-29624200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:29622800-29624600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr6:29622800-29624800	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr6:29622800-29625000	Enhancers	H1 Cell Line	embryonic stem cell
15	chr6:29623200-29624600	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr6:29623200-29625200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr6:29623400-29624400	Enhancers	Stomach Smooth Muscle	stomach
18	chr6:29623400-29624800	Enhancers	Aorta	Aorta
19	chr6:29623400-29625000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:29623400-29630600	Active TSS	Brain Anterior Caudate	brain
21	chr6:29623600-29624400	Flanking Active TSS	GM12878-XiMat	blood
22	chr6:29623600-29624600	Weak transcription	Left Ventricle	heart
23	chr6:29623600-29627200	Active TSS	Brain Hippocampus Middle	brain
24	chr6:29623800-29625000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:29624000-29624200	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:29624000-29624200	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr6:29624000-29624200	Weak transcription	Brain Substantia Nigra	brain
28	chr6:29624000-29624200	Enhancers	Rectal Smooth Muscle	rectum
29	chr6:29624000-29624400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr6:29624000-29624800	Enhancers	H9 Cell Line	embryonic stem cell
31	chr6:29624000-29624800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:29624000-29625000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:29624000-29628000	Active TSS	Brain Angular Gyrus	brain

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