Variant report

Variant	rs6427641
Chromosome Location	chr1:154380486-154380487
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr1:154379487-154380582	GM12878	blood:	n/a	n/a
2	MAX	chr1:154380412-154380597	GM12878	blood:	n/a	n/a
3	MTA3	chr1:154379260-154380836	GM12878	blood:	n/a	n/a
4	FOXA1	chr1:154380400-154381355	HepG2	liver:	n/a	chr1:154380796-154380811 chr1:154381107-154381119
5	MYC	chr1:154380190-154380498	MCF10A-Er-Src	breast:	n/a	n/a
6	FOXA1	chr1:154380415-154380954	T-47D	breast:	n/a	chr1:154380796-154380811
7	FOXM1	chr1:154379424-154380763	GM12878	blood:	n/a	n/a
8	CHD2	chr1:154379663-154380499	GM12878	blood:	n/a	n/a
9	MAZ	chr1:154379700-154380638	GM12878	blood:	n/a	n/a
10	BCLAF1	chr1:154379510-154380522	GM12878	blood:	n/a	chr1:154379949-154379958 chr1:154380155-154380164
11	CEBPB	chr1:154379495-154380979	GM12878	blood:	n/a	n/a
12	BHLHE40	chr1:154379538-154380630	GM12878	blood:	n/a	chr1:154379728-154379744
13	SPI1	chr1:154379265-154380593	GM12878	blood:	n/a	chr1:154380459-154380472 chr1:154379949-154379958
14	POLR2A	chr1:154377491-154380860	MCF10A-Er-Src	breast:	n/a	n/a
15	RUNX3	chr1:154378008-154380714	GM12878	blood:	n/a	n/a
16	CHD1	chr1:154376982-154381411	IMR90	lung:	n/a	n/a
17	NFIC	chr1:154379455-154381177	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:154377502-154382614	MCF10A-Er-Src	breast:	n/a	n/a
19	MXI1	chr1:154377096-154381012	IMR90	lung:	n/a	n/a
20	RUNX3	chr1:154379322-154381160	GM12878	blood:	n/a	n/a
21	FOS	chr1:154380219-154380498	MCF10A-Er-Src	breast:	n/a	chr1:154380346-154380354 chr1:154380347-154380358
22	MTA3	chr1:154378011-154380656	GM12878	blood:	n/a	n/a
23	PML	chr1:154378788-154381090	GM12878	blood:	n/a	n/a
24	MYC	chr1:154379905-154380499	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr1:154377097-154381240	GM18505	blood:	n/a	n/a
26	POLR2A	chr1:154377291-154381193	IMR90	lung:	n/a	n/a
27	EGR1	chr1:154379843-154380508	MCF-7	breast:	n/a	chr1:154380224-154380234 chr1:154380222-154380236 chr1:154380224-154380235 chr1:154380218-154380240 chr1:154380223-154380236 chr1:154380224-154380234 chr1:154379946-154379955
28	POLR2A	chr1:154379563-154381110	GM12891	blood:	n/a	n/a
29	RELA	chr1:154379636-154381225	GM18505	blood:	n/a	n/a
30	RCOR1	chr1:154376980-154381066	IMR90	lung:	n/a	n/a
31	RELA	chr1:154379761-154381086	GM19099	blood:	n/a	n/a
32	STAT5A	chr1:154380456-154381073	GM12878	blood:	n/a	chr1:154380919-154380931 chr1:154380459-154380471
33	FOS	chr1:154380095-154380516	MCF10A-Er-Src	breast:	n/a	chr1:154380346-154380354 chr1:154380347-154380358
34	RELA	chr1:154379610-154381113	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154378359..154380579-chr1:154401148..154402901,2	MCF-7	breast:
2	chr1:154379631..154382392-chr20:55784816..55787372,2	MCF-7	breast:
3	chr1:154154370..154156741-chr1:154377003..154381011,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228013	TF binding region
ENSG00000143549	Chromatin interaction
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10908835	0.82[CEU][hapmap]
rs12127600	0.82[CEU][hapmap]
rs4845617	0.81[CEU][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6427627	0.82[CEU][hapmap]
rs7553271	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs952146	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers 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 target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6427641	SHC1	cis	parietal	SCAN
rs6427641	CCT3	cis	parietal	SCAN
rs6427641	ANXA9	cis	parietal	SCAN
rs6427641	LCE1E	cis	parietal	SCAN
rs6427641	S100A8	cis	parietal	SCAN
rs6427641	HAPLN2	cis	parietal	SCAN
rs6427641	IL6R	cis	lymphoblastoid	seeQTL
rs6427641	SCAMP3	cis	parietal	SCAN
rs6427641	IL6R	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154377000-154381000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr1:154377000-154381200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:154377200-154381200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:154377400-154380800	Flanking Active TSS	HMEC	breast
5	chr1:154377400-154381200	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr1:154377800-154381200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:154378000-154381200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr1:154378200-154380600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr1:154378200-154381000	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr1:154378200-154381000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:154378200-154381400	Flanking Active TSS	GM12878-XiMat	blood
12	chr1:154378200-154382600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr1:154378400-154380600	Enhancers	Fetal Heart	heart
14	chr1:154378400-154380800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:154378400-154381200	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr1:154378600-154380600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:154378600-154381000	Flanking Active TSS	NHEK	skin
18	chr1:154378800-154380600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:154378800-154380800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:154378800-154380800	Flanking Active TSS	NHLF	lung
21	chr1:154378800-154381000	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr1:154378800-154381000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr1:154378800-154381600	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr1:154379000-154381000	Flanking Active TSS	Colon Smooth Muscle	Colon
25	chr1:154379000-154381000	Enhancers	HSMMtube	muscle
26	chr1:154379000-154381200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:154379000-154381200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr1:154379000-154381200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:154379000-154381200	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr1:154379000-154381400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:154379000-154381800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr1:154379000-154381800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr1:154379200-154380800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr1:154379200-154381000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:154379200-154381200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:154379200-154381200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr1:154379200-154381200	Enhancers	Gastric	stomach
38	chr1:154379200-154381400	Enhancers	A549	lung
39	chr1:154379200-154381600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr1:154379200-154382000	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr1:154379400-154380600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:154379400-154380800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:154379400-154380800	Flanking Active TSS	NHDF-Ad	bronchial
44	chr1:154379400-154381200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr1:154379400-154381200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr1:154379400-154381200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr1:154379400-154381200	Bivalent Enhancer	Fetal Muscle Leg	muscle
48	chr1:154379400-154381200	Flanking Active TSS	Rectal Smooth Muscle	rectum
49	chr1:154379400-154381200	Flanking Active TSS	Stomach Mucosa	stomach
50	chr1:154379400-154383000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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