Variant report

Variant	rs6426106
Chromosome Location	chr1:226315232-226315233
allele	G/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	chr1:226313181..226318051-chr1:226333070..226339347,8	MCF-7	breast:
3	chr1:226313378..226317234-chr1:226370614..226375969,8	MCF-7	breast:
4	chr1:226315099..226318031-chr1:226330803..226332605,3	MCF-7	breast:
5	chr1:226247680..226258196-chr1:226306136..226315725,36	MCF-7	breast:

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

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10799335	0.92[JPT][hapmap]
rs10915930	0.92[JPT][hapmap]
rs12060155	0.80[ASN][1000 genomes]
rs12066979	0.82[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs12096737	0.83[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.80[TSI][hapmap];0.80[ASN][1000 genomes]
rs2377470	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28737326	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768543	0.94[CHD][hapmap];0.92[JPT][hapmap]
rs4012723	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61835246	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61835247	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6681021	0.92[JPT][hapmap]
rs6692849	0.80[ASN][1000 genomes]
rs6700189	0.94[CHD][hapmap];0.92[JPT][hapmap]
rs7522361	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6426106	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs6426106	H3F3A	cis	Nerve Tibial	GTEx
rs6426106	LIN9	cis	cerebellum	SCAN
rs6426106	H3F3A	cis	Esophagus Mucosa	GTEx
rs6426106	GJC2	cis	cerebellum	SCAN
rs6426106	ITPKB	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226310400-226333800	Weak transcription	Small Intestine	intestine
2	chr1:226310600-226315400	Weak transcription	HSMM	muscle
3	chr1:226310600-226315400	Weak transcription	HUVEC	blood vessel
4	chr1:226310600-226319800	Weak transcription	Right Ventricle	heart
5	chr1:226310600-226322400	Weak transcription	Right Atrium	heart
6	chr1:226310800-226315400	Weak transcription	Primary T cells from cord blood	blood
7	chr1:226310800-226315400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:226310800-226331200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:226311400-226315600	Weak transcription	Liver	Liver
10	chr1:226311400-226315800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:226312000-226316400	Weak transcription	Gastric	stomach
12	chr1:226312800-226321000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:226313000-226316200	Weak transcription	NHLF	lung
14	chr1:226313000-226316400	Enhancers	Stomach Mucosa	stomach
15	chr1:226313000-226323200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:226313200-226315400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:226313400-226315400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:226313400-226315400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:226313400-226315400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:226313400-226315600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:226313400-226322000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:226313400-226322600	Weak transcription	Brain Angular Gyrus	brain
23	chr1:226313800-226315600	Weak transcription	Spleen	Spleen
24	chr1:226314400-226315400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr1:226314600-226315400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:226314600-226315400	Enhancers	Fetal Intestine Large	intestine
27	chr1:226314600-226316200	Enhancers	Fetal Thymus	thymus
28	chr1:226314600-226316400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:226314600-226316600	Enhancers	Fetal Intestine Small	intestine
30	chr1:226314600-226316800	Enhancers	Pancreas	Pancrea
31	chr1:226314600-226317000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:226314800-226315400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr1:226314800-226316200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:226314800-226316200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
35	chr1:226314800-226316600	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:226314800-226316600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:226314800-226316600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr1:226314800-226316800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:226314800-226316800	Enhancers	HMEC	breast
40	chr1:226314800-226317000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:226315000-226315400	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr1:226315000-226315400	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr1:226315000-226315400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:226315000-226315400	Enhancers	K562	blood
45	chr1:226315000-226315600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr1:226315000-226315600	Enhancers	Primary hematopoietic stem cells	blood
47	chr1:226315000-226315600	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr1:226315000-226315600	Flanking Active TSS	A549	lung
49	chr1:226315000-226315800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:226315000-226315800	Enhancers	Primary T helper naive cells from peripheral blood	blood

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