Variant report

Variant	rs4950380
Chromosome Location	chr1:146637603-146637604
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:146636327..146637904-chr1:146709473..146711189,2	MCF-7	breast:
2	chr1:146633754..146636394-chr1:146637332..146639579,3	K562	blood:
3	chr1:146625650..146629036-chr1:146636126..146639044,3	MCF-7	breast:
4	chr1:146625774..146628182-chr1:146636960..146638871,2	K562	blood:
5	chr1:146637222..146651713-chr1:146712141..146718911,44	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131778	Chromatin interaction
ENSG00000131791	Chromatin interaction
ENSG00000131781	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1036850	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1036851	0.97[ASN][1000 genomes]
rs1036852	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1047140	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10751402	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10793652	0.82[ASN][1000 genomes]
rs10793653	0.82[ASN][1000 genomes]
rs10900314	0.80[EUR][1000 genomes]
rs10900315	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10900321	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10900322	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10900326	0.81[AMR][1000 genomes]
rs11239950	0.82[ASN][1000 genomes]
rs11239951	0.82[ASN][1000 genomes]
rs11578109	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12028924	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12060049	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12094979	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12095014	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12139680	0.82[ASN][1000 genomes]
rs12144240	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1348316	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1442758	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1442760	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17359526	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1837983	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1837984	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1899485	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2014107	0.81[AMR][1000 genomes]
rs2044151	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2354442	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34394205	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34481225	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35143111	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4950307	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4950366	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4950369	0.81[AMR][1000 genomes]
rs4950370	0.81[AMR][1000 genomes]
rs4950372	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4950378	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57405088	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57649470	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6593735	0.82[AMR][1000 genomes]
rs6593738	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6593739	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6668690	0.80[ASN][1000 genomes]
rs6673185	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6680845	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6687016	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6689155	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6693631	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71510593	0.82[ASN][1000 genomes]
rs7552010	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs882344	0.80[EUR][1000 genomes]
rs930495	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757753	chr1:145883119-146697542	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv872251	chr1:146152553-146803630	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
4	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
5	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
6	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
7	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats 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	113 gene(s)	inside rSNPs	diseases
8	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
9	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	111 gene(s)	inside rSNPs	diseases
10	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
11	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
12	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
13	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
14	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
15	nsv872255	chr1:146550780-146969712	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
16	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
17	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
18	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS 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	49 gene(s)	inside rSNPs	diseases
19	nsv1009943	chr1:146618929-146893851	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
20	nsv535132	chr1:146618929-146893851	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4950380	CHD1L	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146624600-146639600	Strong transcription	Primary T cells from cord blood	blood
2	chr1:146624600-146640400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:146624800-146642600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:146625000-146638400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:146625000-146638400	Strong transcription	Duodenum Mucosa	Duodenum
6	chr1:146625200-146638200	Strong transcription	Osteobl	bone
7	chr1:146625200-146638600	Strong transcription	Fetal Muscle Leg	muscle
8	chr1:146625200-146639600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:146625200-146639600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:146625200-146639800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:146625400-146638200	Strong transcription	HepG2	liver
12	chr1:146625400-146638800	Strong transcription	Liver	Liver
13	chr1:146625400-146639200	Strong transcription	Dnd41	blood
14	chr1:146625400-146639400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:146625600-146639200	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:146625800-146639600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr1:146626200-146639600	Weak transcription	Fetal Heart	heart
18	chr1:146627600-146639600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:146628000-146639600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr1:146628800-146639400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:146629000-146639400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:146629400-146639400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:146629800-146640200	Weak transcription	K562	blood
24	chr1:146630000-146641200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:146630800-146640200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:146631600-146642800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:146632000-146639800	Weak transcription	Stomach Mucosa	stomach
28	chr1:146632000-146642400	Weak transcription	Colonic Mucosa	Colon
29	chr1:146632000-146642600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:146632200-146638200	Weak transcription	Esophagus	oesophagus
31	chr1:146632200-146638200	Weak transcription	Pancreas	Pancrea
32	chr1:146632200-146639200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:146632200-146642400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:146632200-146642800	Weak transcription	Gastric	stomach
35	chr1:146632200-146643200	Weak transcription	Spleen	Spleen
36	chr1:146632400-146642000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr1:146632400-146642000	Weak transcription	Fetal Brain Male	brain
38	chr1:146632400-146642200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:146632600-146643000	Weak transcription	Lung	lung
40	chr1:146632800-146642400	Weak transcription	Fetal Kidney	kidney
41	chr1:146633000-146640400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:146633000-146641400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:146633200-146638800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr1:146633200-146639200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:146633200-146641400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr1:146633200-146641800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:146633400-146637800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:146633400-146637800	Weak transcription	HSMMtube	muscle
49	chr1:146633400-146638400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:146633400-146642400	Weak transcription	Thymus	Thymus

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