Variant report

Variant	rs61835246
Chromosome Location	chr1:226314357-226314358
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226247784..226253760-chr1:226305545..226317702,29	MCF-7	breast:
2	chr1:226250361..226252761-chr1:226312416..226314743,2	K562	blood:
3	chr1:226313181..226318051-chr1:226333070..226339347,8	MCF-7	breast:
4	chr1:226245827..226258736-chr1:226304107..226314743,27	K562	blood:
5	chr1:226313378..226317234-chr1:226370614..226375969,8	MCF-7	breast:
6	chr1:226247680..226258196-chr1:226306136..226315725,36	MCF-7	breast:
7	chr1:226313633..226315169-chr1:226374399..226376035,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163041	Chromatin interaction
ENSG00000234478	Chromatin interaction
ENSG00000272562	Chromatin interaction
ENSG00000182827	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12060155	0.84[ASN][1000 genomes]
rs12066979	0.84[ASN][1000 genomes]
rs12096737	0.84[ASN][1000 genomes]
rs2377470	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28737326	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4012723	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61835247	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6426106	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6692849	0.84[ASN][1000 genomes]
rs7522361	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	esv1792510	chr1:226277560-226323824	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs61835246	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs61835246	H3F3A	cis	Esophagus Mucosa	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226310400-226315200	Weak transcription	HSMMtube	muscle
2	chr1:226310400-226333800	Weak transcription	Small Intestine	intestine
3	chr1:226310600-226314600	Weak transcription	Lung	lung
4	chr1:226310600-226315000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:226310600-226315200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:226310600-226315200	Weak transcription	NH-A	brain
7	chr1:226310600-226315400	Weak transcription	HSMM	muscle
8	chr1:226310600-226315400	Weak transcription	HUVEC	blood vessel
9	chr1:226310600-226319800	Weak transcription	Right Ventricle	heart
10	chr1:226310600-226322400	Weak transcription	Right Atrium	heart
11	chr1:226310800-226314600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:226310800-226315200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:226310800-226315200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:226310800-226315400	Weak transcription	Primary T cells from cord blood	blood
15	chr1:226310800-226315400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:226310800-226331200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:226311000-226315000	Enhancers	Primary B cells from peripheral blood	blood
18	chr1:226311000-226315200	Enhancers	Primary B cells from cord blood	blood
19	chr1:226311200-226315000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:226311200-226315000	Weak transcription	Placenta	Placenta
21	chr1:226311400-226315000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:226311400-226315000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:226311400-226315600	Weak transcription	Liver	Liver
24	chr1:226311400-226315800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:226312000-226315000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:226312000-226316400	Weak transcription	Gastric	stomach
27	chr1:226312800-226321000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:226313000-226314800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:226313000-226314800	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr1:226313000-226314800	Weak transcription	HMEC	breast
31	chr1:226313000-226315000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:226313000-226315000	Weak transcription	Fetal Heart	heart
33	chr1:226313000-226315000	Weak transcription	Fetal Lung	lung
34	chr1:226313000-226315200	Weak transcription	Fetal Kidney	kidney
35	chr1:226313000-226316200	Weak transcription	NHLF	lung
36	chr1:226313000-226316400	Enhancers	Stomach Mucosa	stomach
37	chr1:226313000-226323200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:226313200-226315000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:226313200-226315000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:226313200-226315400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:226313400-226314400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:226313400-226314600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:226313400-226314600	Weak transcription	Esophagus	oesophagus
44	chr1:226313400-226314600	Weak transcription	Fetal Intestine Small	intestine
45	chr1:226313400-226314600	Weak transcription	Fetal Thymus	thymus
46	chr1:226313400-226314600	Weak transcription	Pancreas	Pancrea
47	chr1:226313400-226314600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:226313400-226314800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:226313400-226314800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:226313400-226314800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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