Variant report

Variant	rs4926443
Chromosome Location	chr1:246942107-246942108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246934177..246937192-chr1:246941017..246944440,4	K562	blood:
2	chr1:246941558..246944485-chr20:45985608..45987605,2	MCF-7	breast:
3	chr1:246940173..246942753-chr1:246943130..246945283,2	MCF-7	breast:
4	chr1:246929352..246931655-chr1:246940972..246943621,2	K562	blood:
5	chr1:246937235..246940255-chr1:246941352..246944349,3	K562	blood:
6	chr1:246941244..246944008-chr1:246946969..246949951,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227953	Chromatin interaction
ENSG00000260855	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1127098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1127149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12034911	0.81[EUR][1000 genomes]
rs12121187	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12128579	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12129386	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs12129828	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12402095	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403128	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12407065	0.85[EUR][1000 genomes]
rs12409066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410595	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12735300	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3087781	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34048530	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34677128	0.87[ASN][1000 genomes]
rs35021082	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35570407	0.87[ASN][1000 genomes]
rs35736382	0.87[ASN][1000 genomes]
rs3795469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4078128	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41310575	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4926440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4926442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4926444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4926447	0.89[AMR][1000 genomes]
rs4926449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4926450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4926456	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61684731	0.88[ASN][1000 genomes]
rs61852479	0.87[ASN][1000 genomes]
rs61852481	0.88[ASN][1000 genomes]
rs61852482	0.88[ASN][1000 genomes]
rs6426329	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6668806	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6682900	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6689579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6697433	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6697526	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6699332	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6701991	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7365254	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7366187	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs7410830	0.85[ASN][1000 genomes]
rs74152239	0.93[ASN][1000 genomes]
rs7513496	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]
rs7526237	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7528002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7550482	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7551836	1.00[CEU][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes]
rs9659021	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv873423	chr1:246923861-246978504	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv549545	chr1:246936353-246963019	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	esv2756894	chr1:246939856-246946021	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	esv2759013	chr1:246939856-246946021	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4926443	SCCPDH	cis	lymphoblastoid	seeQTL
rs4926443	CGI-49	cis	multi-tissue	Pritchard
rs4926443	SCCPDH	cis	multi-tissue	Pritchard

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
2	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:246895000-246942200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:246904600-246942800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr1:246905000-246945800	Weak transcription	Psoas Muscle	Psoas
7	chr1:246920800-246944200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:246921200-246943200	Strong transcription	Dnd41	blood
9	chr1:246921600-246945800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:246922200-246944600	Strong transcription	Fetal Muscle Trunk	muscle
11	chr1:246923200-246945000	Strong transcription	Fetal Muscle Leg	muscle
12	chr1:246924000-246944200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr1:246924400-246945800	Weak transcription	Primary B cells from cord blood	blood
14	chr1:246925200-246952200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:246928800-246944800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:246932400-246945800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:246932400-246952000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:246932600-246948000	Strong transcription	Liver	Liver
19	chr1:246932600-246948600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:246932600-246948600	Weak transcription	Esophagus	oesophagus
21	chr1:246932800-246945000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:246932800-246945600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:246932800-246945800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:246932800-246948800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:246932800-246952400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:246932800-246956400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:246933200-246945800	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:246934400-246944800	Strong transcription	Fetal Intestine Large	intestine
29	chr1:246934600-246944200	Strong transcription	HSMM	muscle
30	chr1:246937000-246944000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:246938000-246943000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:246938400-246942400	Strong transcription	Fetal Thymus	thymus
33	chr1:246938400-246944200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:246938400-246944400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:246938400-246945800	Strong transcription	Fetal Stomach	stomach
36	chr1:246938400-246947200	Strong transcription	Fetal Intestine Small	intestine
37	chr1:246938600-246942600	Strong transcription	Left Ventricle	heart
38	chr1:246938600-246944600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:246938800-246945000	Strong transcription	Placenta	Placenta
40	chr1:246939000-246943400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:246939000-246944600	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:246939000-246944800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:246939000-246945600	Weak transcription	Fetal Heart	heart
44	chr1:246939200-246942800	Strong transcription	Fetal Brain Female	brain
45	chr1:246939200-246945000	Strong transcription	Stomach Smooth Muscle	stomach
46	chr1:246940200-246945800	Weak transcription	GM12878-XiMat	blood
47	chr1:246940200-246947600	Weak transcription	HUVEC	blood vessel
48	chr1:246940200-246948800	Weak transcription	Fetal Brain Male	brain
49	chr1:246940400-246943200	Weak transcription	Brain Substantia Nigra	brain
50	chr1:246940400-246944000	Weak transcription	A549	lung

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