Variant report

Variant	rs4950379
Chromosome Location	chr1:146637585-146637586
allele	C/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: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs11800580	0.83[AMR][1000 genomes]
rs11809339	0.85[ASN][1000 genomes]
rs11811023	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12046706	0.92[EUR][1000 genomes]
rs12725189	0.85[ASN][1000 genomes]
rs17159914	0.92[EUR][1000 genomes]
rs17159924	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17160051	0.83[AMR][1000 genomes]
rs17355398	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17355419	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17355474	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17355509	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17356184	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17356219	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17356233	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17356240	1.00[AFR][1000 genomes]
rs17359629	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17360443	1.00[AFR][1000 genomes]
rs1813002	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1822309	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1932977	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1999820	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2008414	0.92[ASN][1000 genomes]
rs2014106	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2083720	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2354428	1.00[AFR][1000 genomes]
rs28381210	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2883434	0.91[EUR][1000 genomes]
rs3737855	0.82[AMR][1000 genomes]
rs3766519	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766520	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766522	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4301678	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4593887	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4950304	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4950305	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4950306	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4950308	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4950313	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4950315	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4950316	1.00[AFR][1000 genomes]
rs4950367	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4950371	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4950373	0.92[ASN][1000 genomes]
rs4950382	0.92[EUR][1000 genomes]
rs4950384	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4950389	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4950392	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4950415	1.00[AFR][1000 genomes]
rs55697094	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55791847	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs55799799	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55828524	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs55963049	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56012243	0.85[ASN][1000 genomes]
rs56080828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56151278	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56198825	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56864370	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61838936	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61838937	0.85[ASN][1000 genomes]
rs61838938	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61838944	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61838945	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61838947	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61838951	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6660507	0.88[EUR][1000 genomes]
rs718369	0.80[EUR][1000 genomes]
rs72691004	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72691012	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72691016	0.83[AMR][1000 genomes]
rs72691032	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs72691033	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs72691041	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs72691054	1.00[AFR][1000 genomes]
rs72706428	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72706441	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72706444	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72708536	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7514808	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7514970	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7515160	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7523975	0.85[ASN][1000 genomes]
rs7538682	0.86[EUR][1000 genomes]
rs7541393	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs972368	0.90[AMR][1000 genomes];0.86[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
rs4950379	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	chr1:146624200-146637600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:146624600-146639600	Strong transcription	Primary T cells from cord blood	blood
3	chr1:146624600-146640400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:146624800-146637600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:146624800-146642600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:146625000-146638400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:146625000-146638400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr1:146625200-146638200	Strong transcription	Osteobl	bone
9	chr1:146625200-146638600	Strong transcription	Fetal Muscle Leg	muscle
10	chr1:146625200-146639600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:146625200-146639600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:146625200-146639800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr1:146625400-146638200	Strong transcription	HepG2	liver
14	chr1:146625400-146638800	Strong transcription	Liver	Liver
15	chr1:146625400-146639200	Strong transcription	Dnd41	blood
16	chr1:146625400-146639400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:146625600-146639200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:146625800-146639600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr1:146626200-146639600	Weak transcription	Fetal Heart	heart
20	chr1:146627600-146639600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:146628000-146639600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr1:146628800-146639400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:146629000-146639400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:146629400-146639400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:146629800-146640200	Weak transcription	K562	blood
26	chr1:146630000-146641200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:146630800-146637600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr1:146630800-146640200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr1:146631600-146642800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:146632000-146639800	Weak transcription	Stomach Mucosa	stomach
31	chr1:146632000-146642400	Weak transcription	Colonic Mucosa	Colon
32	chr1:146632000-146642600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:146632200-146638200	Weak transcription	Esophagus	oesophagus
34	chr1:146632200-146638200	Weak transcription	Pancreas	Pancrea
35	chr1:146632200-146639200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:146632200-146642400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:146632200-146642800	Weak transcription	Gastric	stomach
38	chr1:146632200-146643200	Weak transcription	Spleen	Spleen
39	chr1:146632400-146642000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:146632400-146642000	Weak transcription	Fetal Brain Male	brain
41	chr1:146632400-146642200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:146632600-146643000	Weak transcription	Lung	lung
43	chr1:146632800-146642400	Weak transcription	Fetal Kidney	kidney
44	chr1:146633000-146640400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:146633000-146641400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:146633200-146638800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr1:146633200-146639200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:146633200-146641400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:146633200-146641800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:146633400-146637600	Weak transcription	Placenta	Placenta

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