Variant report

Variant	rs3768543
Chromosome Location	chr1:226253926-226253927
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:226253754-226254595	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr1:226248810-226256763	K562	blood:	n/a	n/a
3	POLR2A	chr1:226253843-226254736	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:226253889-226254444	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:226253892-226254631	K562	blood:	n/a	n/a
6	POLR2A	chr1:226252358-226255036	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:226253910-226254191	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:226253831-226254551	GM12892	blood:	n/a	n/a
9	POLR2A	chr1:226253696-226254111	A549	lung:	n/a	n/a
10	RFX5	chr1:226253587-226255011	SK-N-SH	brain:	n/a	chr1:226254507-226254522
11	TBL1XR1	chr1:226253550-226253935	K562	blood:	n/a	n/a
12	POLR2A	chr1:226253833-226254698	GM12878	blood:	n/a	n/a
13	MXI1	chr1:226253905-226254004	GM12878	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226252953..226257459-chr1:226295699..226299600,6	K562	blood:
2	chr1:226183087..226192322-chr1:226243551..226254243,95	K562	blood:
3	chr1:226247680..226258196-chr1:226306136..226315725,36	MCF-7	breast:
4	chr1:226252549..226256033-chr1:226258651..226261482,3	MCF-7	breast:
5	chr1:226252321..226254478-chr1:226297571..226300117,4	MCF-7	breast:
6	chr1:226184876..226191468-chr1:226247585..226254254,12	MCF-7	breast:
7	chr1:226252587..226254358-chr1:226261126..226263973,2	MCF-7	breast:
8	chr1:226252003..226254047-chr1:226372639..226375517,2	MCF-7	breast:
9	chr1:226248537..226252087-chr1:226252328..226257854,13	MCF-7	breast:
10	chr1:226252767..226255693-chr1:226262385..226264510,2	MCF-7	breast:
11	chr1:226248851..226254336-chr1:226269112..226274282,12	MCF-7	breast:
12	chr1:226178791..226193771-chr1:226246813..226256535,111	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272562	TF binding region
ENSG00000182827	Chromatin interaction
ENSG00000272562	Chromatin interaction
ENSG00000225518	Chromatin interaction
ENSG00000143751	Chromatin interaction
ENSG00000270598	Chromatin interaction
ENSG00000163041	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10799335	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10915930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10915931	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10915932	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12060155	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12066979	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12086044	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12096468	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12096737	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4271181	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6426106	0.94[CHD][hapmap];0.92[JPT][hapmap]
rs6678547	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6681021	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6692329	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6692849	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6700189	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7543135	0.88[AMR][1000 genomes];0.87[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	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3768543	ACBD3	cis	parietal	SCAN
rs3768543	H3F3A	cis	Artery Tibial	GTEx
rs3768543	H3F3A	cis	lung	GTEx
rs3768543	H3F3A	cis	Whole Blood	GTEx
rs3768543	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs3768543	H3F3A	cis	Esophagus Mucosa	GTEx
rs3768543	H3F3A	cis	Esophagus Muscularis	GTEx
rs3768543	H3F3A	cis	Nerve Tibial	GTEx
rs3768543	H3F3A	cis	Adipose Subcutaneous	GTEx
rs3768543	H3F3A	cis	Muscle Skeletal	GTEx
rs3768543	H3F3A	cis	Artery Aorta	GTEx
rs3768543	H3F3A	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226251600-226254000	Weak transcription	Spleen	Spleen
2	chr1:226251800-226254400	Weak transcription	Gastric	stomach
3	chr1:226252200-226254000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:226252200-226254000	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr1:226252200-226254000	Weak transcription	Pancreas	Pancrea
6	chr1:226252200-226254000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:226252200-226254200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
8	chr1:226252200-226255200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
9	chr1:226252200-226256000	Weak transcription	Lung	lung
10	chr1:226252200-226256400	Weak transcription	Esophagus	oesophagus
11	chr1:226252200-226257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:226252400-226254400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
13	chr1:226252400-226254600	Transcr. at gene 5' and 3'	Dnd41	blood
14	chr1:226252400-226256400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:226252600-226254400	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
16	chr1:226252600-226254600	Transcr. at gene 5' and 3'	Hela-S3	cervix
17	chr1:226252600-226255000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:226252800-226254000	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
19	chr1:226252800-226254200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:226252800-226254600	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:226252800-226254600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
22	chr1:226252800-226255000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:226252800-226257400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:226253000-226254200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr1:226253000-226254200	Genic enhancers	NHDF-Ad	bronchial
26	chr1:226253000-226254600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
27	chr1:226253000-226254600	Genic enhancers	HSMM	muscle
28	chr1:226253000-226254600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
29	chr1:226253000-226255800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:226253000-226257600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:226253000-226258000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:226253000-226270400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:226253200-226254000	Genic enhancers	K562	blood
34	chr1:226253200-226254000	Genic enhancers	Osteobl	bone
35	chr1:226253200-226254200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:226253200-226254400	Genic enhancers	Fetal Kidney	kidney
37	chr1:226253200-226254600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:226253200-226254600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:226253200-226254600	Genic enhancers	Brain Anterior Caudate	brain
40	chr1:226253200-226254600	Genic enhancers	Fetal Muscle Leg	muscle
41	chr1:226253200-226254600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
42	chr1:226253200-226254600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
43	chr1:226253200-226254600	Genic enhancers	A549	lung
44	chr1:226253200-226254600	Genic enhancers	HepG2	liver
45	chr1:226253200-226254800	Genic enhancers	Fetal Stomach	stomach
46	chr1:226253200-226255400	Genic enhancers	Primary monocytes fromperipheralblood	blood
47	chr1:226253200-226255400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:226253200-226256400	Genic enhancers	Rectal Mucosa Donor 29	rectum
49	chr1:226253200-226256600	Genic enhancers	Colon Smooth Muscle	Colon
50	chr1:226253200-226256600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

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