Variant report

Variant	rs6427640
Chromosome Location	chr1:153632852-153632853
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153579256..153583611-chr1:153630358..153635573,4	MCF-7	breast:
2	chr1:153605696..153608522-chr1:153629929..153633320,6	MCF-7	breast:
3	chr1:153597855..153601076-chr1:153629883..153633781,4	MCF-7	breast:
4	chr1:153631452..153634025-chr1:153753430..153756268,2	MCF-7	breast:
5	chr1:153632026..153634046-chr17:57922237..57924037,2	MCF-7	breast:
6	chr1:153503911..153505890-chr1:153631477..153634216,2	K562	blood:
7	chr1:153632004..153633791-chr1:153723547..153726062,2	K562	blood:

Variant related genes	Relation type
ENSG00000189171	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000233222	Chromatin interaction
ENSG00000243613	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000188643	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1046381	0.94[EUR][1000 genomes]
rs10797056	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10797090	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10797096	0.87[ASN][1000 genomes]
rs10908746	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10908848	0.85[ASN][1000 genomes]
rs11265625	0.87[ASN][1000 genomes]
rs11265633	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1128894	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11580122	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11588347	0.85[ASN][1000 genomes]
rs12139953	0.91[ASN][1000 genomes]
rs12564925	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12730186	0.87[ASN][1000 genomes]
rs1810836	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1888115	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2274739	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2274740	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28379831	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28380060	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28416529	0.81[EUR][1000 genomes]
rs28510471	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28518786	0.81[ASN][1000 genomes]
rs28580554	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28613361	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28700217	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3790412	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3795396	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3806234	0.92[ASN][1000 genomes]
rs3818632	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3828031	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3862047	0.92[ASN][1000 genomes]
rs4351684	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845557	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845558	0.84[EUR][1000 genomes]
rs4845560	0.86[EUR][1000 genomes]
rs4845563	0.91[ASN][1000 genomes]
rs4845564	0.84[ASN][1000 genomes]
rs55772653	0.87[ASN][1000 genomes]
rs66721814	0.91[ASN][1000 genomes]
rs6674929	0.84[ASN][1000 genomes]
rs7345	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7934	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs913860	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs913861	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9661993	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9662664	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv547928	chr1:153612133-153714252	Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
11	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
12	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
15	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
16	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6427640	RP1-178F15.4	cis	Artery Tibial	GTEx
rs6427640	RP1-178F15.4	cis	Heart Left Ventricle	GTEx
rs6427640	RP1-178F15.4	cis	Skin Sun Exposed Lower leg	GTEx
rs6427640	RP1-178F15.4	cis	lung	GTEx
rs6427640	CHTOP	cis	Muscle Skeletal	GTEx
rs6427640	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs6427640	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs6427640	RP1-178F15.4	cis	Artery Aorta	GTEx
rs6427640	S100A13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153632000-153633600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:153632000-153633600	Weak transcription	Gastric	stomach
3	chr1:153632000-153633600	Weak transcription	Small Intestine	intestine
4	chr1:153632000-153633800	Weak transcription	Ovary	ovary
5	chr1:153632000-153634800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:153632000-153642200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:153632000-153642800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:153632200-153633200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:153632200-153633200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:153632200-153633400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:153632200-153633400	Weak transcription	NHDF-Ad	bronchial
12	chr1:153632200-153633400	Weak transcription	NHEK	skin
13	chr1:153632200-153633600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:153632200-153633600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:153632200-153633600	Weak transcription	Psoas Muscle	Psoas
16	chr1:153632200-153633600	Weak transcription	HSMMtube	muscle
17	chr1:153632200-153633800	Weak transcription	Aorta	Aorta
18	chr1:153632200-153633800	Weak transcription	Fetal Kidney	kidney
19	chr1:153632200-153633800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:153632400-153633000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:153632400-153633200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:153632400-153633200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:153632400-153633200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:153632400-153633200	Weak transcription	Primary B cells from cord blood	blood
25	chr1:153632400-153633200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:153632400-153633200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:153632400-153633200	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:153632400-153633200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:153632400-153633200	Weak transcription	Left Ventricle	heart
30	chr1:153632400-153633200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:153632400-153633200	Weak transcription	Right Ventricle	heart
32	chr1:153632400-153633200	Weak transcription	HSMM	muscle
33	chr1:153632400-153633200	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr1:153632400-153633400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:153632400-153633400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:153632400-153633400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:153632400-153633400	Weak transcription	Brain Anterior Caudate	brain
38	chr1:153632400-153633400	Weak transcription	Pancreas	Pancrea
39	chr1:153632400-153633400	Weak transcription	GM12878-XiMat	blood
40	chr1:153632400-153633600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:153632400-153633600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:153632400-153633600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:153632400-153633600	Weak transcription	Brain Substantia Nigra	brain
44	chr1:153632400-153633600	Weak transcription	Colonic Mucosa	Colon
45	chr1:153632400-153633600	Weak transcription	Esophagus	oesophagus
46	chr1:153632400-153633600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr1:153632400-153633600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr1:153632400-153633600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:153632400-153633600	Weak transcription	Spleen	Spleen
50	chr1:153632400-153633600	Weak transcription	A549	lung

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