Variant report

Variant	rs1127827
Chromosome Location	chr5:128430757-128430758
allele	C/T
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	MYC	chr5:128429734-128431566	K562	blood:	n/a	chr5:128431028-128431037 chr5:128430990-128430999
2	POLR2A	chr5:128429739-128431146	H1-neurons	neurons:	n/a	n/a
3	MAX	chr5:128429833-128431388	GM12878	blood:	n/a	chr5:128431028-128431037 chr5:128430990-128430999
4	USF2	chr5:128430702-128431189	HepG2	liver:	n/a	n/a
5	RFX5	chr5:128429978-128431468	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr5:128429904-128431141	HepG2	liver:	n/a	n/a
7	SMARCB1	chr5:128429859-128431293	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr5:128429718-128431221	GM12878	blood:	n/a	chr5:128429887-128429908 chr5:128430207-128430220 chr5:128429892-128429910
9	POLR2A	chr5:128430213-128431077	GM12878	blood:	n/a	n/a
10	CTCF	chr5:128430736-128430774	GM12891	blood:	n/a	n/a
11	NRF1	chr5:128430716-128431041	GM12878	blood:	n/a	n/a
12	ZKSCAN1	chr5:128430510-128431032	Hela-S3	cervix:	n/a	n/a
13	MAX	chr5:128429829-128431318	K562	blood:	n/a	chr5:128431028-128431037 chr5:128430990-128430999
14	SIN3AK20	chr5:128430089-128430772	PANC-1	pancreas:	n/a	n/a
15	TCF12	chr5:128430676-128431197	GM12878	blood:	n/a	chr5:128430972-128430982
16	YY1	chr5:128430344-128431141	A549	lung:	n/a	chr5:128430984-128430993 chr5:128430387-128430401 chr5:128430455-128430467 chr5:128430398-128430412 chr5:128430402-128430413
17	SMC3	chr5:128429772-128431274	Hela-S3	cervix:	n/a	n/a
18	ELF1	chr5:128430704-128431246	GM12878	blood:	n/a	n/a
19	SIN3A	chr5:128430340-128431330	GM12878	blood:	n/a	chr5:128431013-128431022 chr5:128430972-128430985
20	CTBP2	chr5:128429794-128431189	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr5:128429911-128431122	GM12878	blood:	n/a	n/a
22	CEBPB	chr5:128430676-128431186	HepG2	liver:	n/a	n/a
23	POLR2A	chr5:128429777-128431327	K562	blood:	n/a	n/a
24	POLR2A	chr5:128430198-128431174	GM12891	blood:	n/a	n/a
25	RUNX3	chr5:128429726-128431367	GM12878	blood:	n/a	n/a
26	CEBPB	chr5:128430729-128431134	K562	blood:	n/a	n/a
27	TAF1	chr5:128429745-128431103	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr5:128429793-128431149	MCF-7	breast:	n/a	n/a
29	ELF1	chr5:128430654-128431137	HepG2	liver:	n/a	n/a
30	CEBPD	chr5:128430755-128431019	HepG2	liver:	n/a	n/a
31	MYBL2	chr5:128429842-128431254	HepG2	liver:	n/a	n/a
32	POLR2A	chr5:128430061-128431132	IMR90	lung:	n/a	n/a
33	CHD1	chr5:128430137-128431243	GM12878	blood:	n/a	chr5:128430167-128430177 chr5:128430321-128430331
34	ETS1	chr5:128430714-128431132	K562	blood:	n/a	chr5:128430982-128430993
35	CEBPD	chr5:128430275-128431149	HepG2	liver:	n/a	n/a
36	TAF1	chr5:128429839-128431015	K562	blood:	n/a	n/a
37	POLR2A	chr5:128429828-128431013	K562	blood:	n/a	n/a
38	MTA3	chr5:128430610-128431277	GM12878	blood:	n/a	n/a
39	TAF1	chr5:128430735-128431076	GM12878	blood:	n/a	n/a
40	ZBTB7A	chr5:128429946-128431274	ECC-1	luminal epithelium:	n/a	chr5:128430346-128430353
41	POLR2A	chr5:128429777-128431258	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr5:128429900-128431128	A549	lung:	n/a	n/a
43	RCOR1	chr5:128429821-128431539	Hela-S3	cervix:	n/a	n/a
44	TAF1	chr5:128429791-128431033	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr5:128430278-128430998	HepG2	liver:	n/a	n/a
46	CTCF	chr5:128430740-128430890	HCFaa	heart:	n/a	n/a
47	CEBPB	chr5:128430662-128431200	A549	lung:	n/a	n/a
48	RAD21	chr5:128429704-128430760	H1-hESC	embryonic stem cell:	n/a	chr5:128429890-128429909 chr5:128429892-128429904
49	EP300	chr5:128430184-128431112	GM12878	blood:	n/a	chr5:128430296-128430312 chr5:128430973-128430989 chr5:128430223-128430239
50	POLR2A	chr5:128429435-128431501	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:67260767..67261329-chr5:128430498..128431009,2	Hela-S3	cervix:
2	chr5:128430725..128432817-chr5:128449870..128452474,3	K562	blood:
3	chr14:100070050..100071046-chr5:128430184..128430973,2	Hela-S3	cervix:
4	chr5:128299750..128303179-chr5:128428591..128431385,3	MCF-7	breast:
5	chr5:60627981..60628508-chr5:128430013..128430866,2	HCT-116	colon:
6	chr5:128430676..128433007-chr5:128447278..128450183,2	K562	blood:
7	chr5:128426917..128432397-chr5:128432508..128439991,15	K562	blood:
8	chr5:128241322..128241829-chr5:128430596..128431143,2	MCF-7	breast:
9	chr5:128429058..128432172-chr5:128432458..128435695,7	MCF-7	breast:

Variant related genes	Relation type
MIR4633	TF binding region
ENSG00000125122	Chromatin interaction
ENSG00000130449	Chromatin interaction
ENSG00000247970	Chromatin interaction
ENSG00000113396	Chromatin interaction
ENSG00000237102	Chromatin interaction
ENSG00000205476	Chromatin interaction
ENSG00000168701	Chromatin interaction
ENSG00000264563	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10036277	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10071265	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1181955	0.81[EUR][1000 genomes]
rs11960471	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13181777	0.80[EUR][1000 genomes]
rs2112697	0.84[AMR][1000 genomes]
rs2161403	0.82[AMR][1000 genomes]
rs2194149	0.81[AMR][1000 genomes]
rs2312251	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2430194	0.96[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2430195	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs257911	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs257912	0.95[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs257919	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3798115	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3798116	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3798117	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3798120	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3822830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3822832	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4141014	0.81[EUR][1000 genomes]
rs4836444	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58498861	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6595879	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6595885	0.82[AMR][1000 genomes]
rs6867600	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6868228	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6871	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6881138	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6888909	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7714427	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7733245	0.81[AMR][1000 genomes]
rs963677	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830485	chr5:128298622-128480492	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv882842	chr5:128301971-128552706	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv599701	chr5:128328165-128773052	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1015525	chr5:128335133-128443859	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription 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	12 gene(s)	inside rSNPs	diseases
5	nsv882847	chr5:128368505-128665719	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
6	nsv882848	chr5:128378225-128516629	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1127827	SHROOM1	cis	cerebellum	SCAN
rs1127827	FNIP1	cis	parietal	SCAN
rs1127827	SLC27A6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:128429400-128431200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:128429400-128431200	Active TSS	Brain Germinal Matrix	brain
3	chr5:128429400-128431200	Active TSS	Fetal Lung	lung
4	chr5:128429400-128431400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr5:128429400-128431400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr5:128429400-128431400	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr5:128429400-128431600	Active TSS	Fetal Kidney	kidney
8	chr5:128429600-128430800	Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr5:128429600-128431000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr5:128429600-128431000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:128429600-128431000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:128429600-128431000	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr5:128429600-128431200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:128429600-128431200	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr5:128429600-128431200	Active TSS	Brain Anterior Caudate	brain
16	chr5:128429600-128431200	Active TSS	Fetal Intestine Small	intestine
17	chr5:128429600-128431200	Active TSS	Rectal Mucosa Donor 31	rectum
18	chr5:128429600-128431200	Active TSS	HMEC	breast
19	chr5:128429600-128431200	Active TSS	NH-A	brain
20	chr5:128429600-128431400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:128429600-128431400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr5:128429600-128431400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:128429600-128431400	Active TSS	Brain Cingulate Gyrus	brain
24	chr5:128429600-128431400	Active TSS	Brain Hippocampus Middle	brain
25	chr5:128429600-128431400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:128429600-128431400	Active TSS	Colon Smooth Muscle	Colon
27	chr5:128429600-128431400	Active TSS	NHEK	skin
28	chr5:128429600-128431600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:128429600-128431600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:128429600-128431600	Active TSS	Fetal Brain Male	brain
31	chr5:128429600-128431800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:128429600-128431800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:128429600-128431800	Active TSS	Fetal Brain Female	brain
34	chr5:128429600-128432000	Active TSS	Fetal Intestine Large	intestine
35	chr5:128429600-128432000	Active TSS	Ovary	ovary
36	chr5:128429600-128432000	Active TSS	K562	blood
37	chr5:128429600-128432600	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr5:128429600-128432600	Active TSS	Fetal Muscle Trunk	muscle
39	chr5:128429600-128433400	Active TSS	Fetal Stomach	stomach
40	chr5:128429800-128431000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr5:128429800-128431000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:128429800-128431000	Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr5:128429800-128431200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr5:128429800-128431200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:128429800-128431200	Active TSS	Brain Angular Gyrus	brain
46	chr5:128429800-128431200	Active TSS	Rectal Smooth Muscle	rectum
47	chr5:128429800-128431200	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr5:128429800-128431200	Active TSS	NHDF-Ad	bronchial
49	chr5:128429800-128431200	Active TSS	NHLF	lung
50	chr5:128429800-128431400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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