Variant report

Variant	rs4727040
Chromosome Location	chr7:140393176-140393177
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:140393175-140393225	Hela-S3	cervix:	n/a
2	chr7:140393175-140393225	AG09319	gingival:	n/a
3	chr7:140393175-140393225	HEEpiC	esophagus:	n/a
4	chr7:140393175-140393225	HL-60	blood:	n/a
5	chr7:140393175-140393225	PFSK-1	brain:	n/a
6	chr7:140393175-140393225	HUVEC	blood vessel:	n/a
7	chr7:140393175-140393225	GM12878	blood:	n/a
8	chr7:140393175-140393225	GM06990	blood:	n/a
9	chr7:140393175-140393225	T-47D	breast:	n/a
10	chr7:140393175-140393225	SK-N-SH	brain:	n/a
11	chr7:140393175-140393225	LNCaP	prostate:	n/a
12	chr7:140393175-140393225	Caco-2	colon:	n/a
13	chr7:140393175-140393225	SAEC	small airway:	n/a
14	chr7:140393175-140393225	Hepatocyte	liver:	n/a
15	chr7:140393175-140393225	HNPCEpiC	eye:	n/a
16	chr7:140393175-140393225	SKMC	muscle:	n/a
17	chr7:140393175-140393225	GM19239	blood:	n/a
18	chr7:140393175-140393225	IMR90	lung:	fetal
19	chr7:140393175-140393225	HCT-116	colon:	n/a
20	chr7:140393175-140393225	AG04449	skin:	fetal
21	chr7:140393175-140393225	H1-hESC	embryonic stem cell:	embryo
22	chr7:140393175-140393225	SK-N-MC	brain:	n/a
23	chr7:140393175-140393225	AG10803	skin:	n/a
24	chr7:140393175-140393225	BJ	skin:	n/a
25	chr7:140393175-140393225	HRPEpiC	eye:	n/a
26	chr7:140393175-140393225	HepG2	liver:	n/a
27	chr7:140393175-140393225	U87	brain:	n/a
28	chr7:140393175-140393225	K562	blood:	n/a
29	chr7:140393175-140393225	A549	lung:	n/a
30	chr7:140393175-140393225	PANC-1	pancreas:	n/a
31	chr7:140393175-140393225	RPTEC	kidney:	n/a
32	chr7:140393175-140393225	ECC-1	luminal epithelium:	n/a
33	chr7:140393175-140393225	HCM	heart:	n/a
34	chr7:140393175-140393225	HMEC	breast:	n/a
35	chr7:140393175-140393225	ProgFib	skin:	n/a
36	chr7:140393175-140393225	HPAEpiC	pulmonary alveolar:	n/a
37	chr7:140393175-140393225	HRCEpiC	kidney:	n/a
38	chr7:140393175-140393225	AoSMC	blood vessel:	n/a
39	chr7:140393175-140393225	HCPEpiC	choroid plexus:	n/a
40	chr7:140393175-140393225	ovcar-3	ovarian:	n/a
41	chr7:140393175-140393225	SK-N-SH_RA	brain:	n/a
42	chr7:140393175-140393225	NHBE	bronchial:	n/a
43	chr7:140393175-140393225	PrEC	prostate:	n/a
44	chr7:140393175-140393225	Jurkat	blood:	n/a
45	chr7:140393175-140393225	HRE	kidney:	n/a
46	chr7:140393175-140393225	BE2_C	brain:	n/a
47	chr7:140393175-140393225	AG04450	lung:	fetal
48	chr7:140393175-140393225	HIPEpiC	eye:	n/a
49	chr7:140393175-140393225	AG09309	skin:	n/a
50	chr7:140393175-140393225	MCF-7	breast:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:140388305..140391159-chr7:140391450..140393273,2	K562	blood:
2	chr7:140370608..140383131-chr7:140387718..140398587,28	MCF-7	breast:

No data

Variant related genes	Relation type
NDUFB2	CpG island
ENSG00000133597	Chromatin interaction
ENSG00000090266	Chromatin interaction
ENSG00000146966	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10241711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10242534	0.81[EUR][1000 genomes]
rs10260676	0.83[ASN][1000 genomes]
rs10269699	0.88[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs1046515	0.83[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1140034	0.83[CHB][hapmap]
rs12375245	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267600	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1267601	0.88[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs1267606	0.88[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs1267609	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1267611	0.88[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs1267613	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1267614	0.88[CEU][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1267617	0.84[EUR][1000 genomes]
rs1267619	0.88[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs1267636	0.88[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs1267638	0.88[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1267639	0.81[EUR][1000 genomes]
rs1267640	0.84[EUR][1000 genomes]
rs1267642	0.88[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1267643	0.83[CHB][hapmap]
rs1267644	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1267649	0.88[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1270193	0.84[EUR][1000 genomes]
rs1639675	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1639678	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1639679	0.88[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs17161666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17161668	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17161750	0.88[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs1733827	0.88[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1733832	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1812162	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2245716	0.84[EUR][1000 genomes]
rs2364393	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs2364394	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs2364396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2364397	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs2364398	0.92[GIH][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2535951	0.88[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs28517771	0.88[ASN][1000 genomes]
rs28577882	0.84[EUR][1000 genomes]
rs2907950	0.83[ASN][1000 genomes]
rs2930315	0.85[ASN][1000 genomes]
rs2930318	0.85[ASN][1000 genomes]
rs2930319	0.85[ASN][1000 genomes]
rs2968549	0.84[ASN][1000 genomes]
rs2968550	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[ASN][1000 genomes]
rs2968551	0.87[ASN][1000 genomes]
rs2968553	1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[ASN][1000 genomes]
rs2968555	0.83[ASN][1000 genomes]
rs2968559	0.83[CHB][hapmap]
rs4725799	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4727011	0.83[CHB][hapmap]
rs4727021	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4727036	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4727041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727053	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6464036	0.88[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs6464123	0.88[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs6464937	0.83[CHB][hapmap]
rs6464984	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6949396	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6962426	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6967652	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6969779	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6977834	0.84[ASN][1000 genomes]
rs73489531	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73489562	0.84[EUR][1000 genomes]
rs73491672	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73491871	0.84[EUR][1000 genomes]
rs73505645	0.88[ASN][1000 genomes]
rs73505647	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7792746	0.83[CHB][hapmap];0.89[GIH][hapmap];0.89[ASN][1000 genomes]
rs7794857	0.81[ASN][1000 genomes]
rs7803697	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831157	chr7:140241339-140426876	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv3351231	chr7:140390303-140588539	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv831158	chr7:140392222-140602315	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4727040	BRAF	Cis_1M	lymphoblastoid	RTeQTL
rs4727040	NDUFB2	cis	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140373800-140395600	Weak transcription	NH-A	brain
2	chr7:140373800-140395800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:140373800-140396000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:140374000-140395800	Weak transcription	Fetal Lung	lung
5	chr7:140374000-140395800	Weak transcription	Right Atrium	heart
6	chr7:140374200-140395800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:140374200-140396000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr7:140374200-140396000	Weak transcription	Psoas Muscle	Psoas
9	chr7:140374400-140395600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr7:140374400-140396200	Weak transcription	Small Intestine	intestine
11	chr7:140374600-140395600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr7:140374600-140395600	Weak transcription	A549	lung
13	chr7:140374600-140395800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr7:140374600-140395800	Weak transcription	Fetal Kidney	kidney
15	chr7:140374800-140395800	Weak transcription	Stomach Mucosa	stomach
16	chr7:140375400-140394600	Weak transcription	Osteobl	bone
17	chr7:140375400-140395400	Strong transcription	Fetal Stomach	stomach
18	chr7:140375400-140395600	Weak transcription	HMEC	breast
19	chr7:140375600-140395600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr7:140375600-140395600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr7:140375600-140395800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr7:140375800-140395600	Weak transcription	Fetal Brain Male	brain
23	chr7:140375800-140395800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr7:140375800-140395800	Weak transcription	NHDF-Ad	bronchial
25	chr7:140376000-140393200	Strong transcription	Placenta	Placenta
26	chr7:140376000-140395600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr7:140376000-140395800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr7:140376200-140393400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:140376600-140395800	Weak transcription	GM12878-XiMat	blood
30	chr7:140376800-140395600	Strong transcription	Fetal Intestine Small	intestine
31	chr7:140377400-140394400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr7:140377600-140393200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr7:140377800-140394800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:140377800-140394800	Strong transcription	Thymus	Thymus
35	chr7:140379000-140395800	Weak transcription	HepG2	liver
36	chr7:140379200-140395600	Weak transcription	Hela-S3	cervix
37	chr7:140381000-140395600	Weak transcription	K562	blood
38	chr7:140381000-140395800	Weak transcription	Colon Smooth Muscle	Colon
39	chr7:140383000-140393400	Strong transcription	Duodenum Mucosa	Duodenum
40	chr7:140383400-140395800	Weak transcription	HSMM	muscle
41	chr7:140383800-140393400	Strong transcription	Fetal Brain Female	brain
42	chr7:140383800-140396000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr7:140383800-140396400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr7:140384200-140393200	Strong transcription	Fetal Muscle Leg	muscle
45	chr7:140384200-140395800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:140384200-140395800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr7:140384200-140396200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:140384400-140395800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr7:140384400-140395800	Weak transcription	HSMMtube	muscle
50	chr7:140384600-140395600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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