Variant report

Variant	rs11769769
Chromosome Location	chr7:128312450-128312451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:128311889-128314146	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr7:128312258-128312487	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr7:128311980-128313921	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:128312406-128312456	HRPEpiC	eye:	n/a
2	chr7:128312406-128312456	HEK293	kidney:	embryo
3	chr7:128312406-128312456	SK-N-MC	brain:	n/a
4	chr7:128312406-128312456	MCF10A-Er-Src	breast:	n/a
5	chr7:128312406-128312456	CMK	blood:	n/a
6	chr7:128312406-128312456	NHBE	bronchial:	n/a
7	chr7:128312406-128312456	HEEpiC	esophagus:	n/a
8	chr7:128312406-128312456	PrEC	prostate:	n/a
9	chr7:128312406-128312456	Caco-2	colon:	n/a
10	chr7:128312406-128312456	AG04450	lung:	fetal
11	chr7:128312406-128312456	NT2-D1	testis:	n/a
12	chr7:128312406-128312456	GM19239	blood:	n/a
13	chr7:128312406-128312456	HL-60	blood:	n/a
14	chr7:128312406-128312456	HUVEC	blood vessel:	n/a
15	chr7:128312406-128312456	LNCaP	prostate:	n/a
16	chr7:128312406-128312456	AG09309	skin:	n/a
17	chr7:128312406-128312456	H1-hESC	embryonic stem cell:	embryo
18	chr7:128312406-128312456	NB4	blood:	n/a
19	chr7:128312406-128312456	HMEC	breast:	n/a
20	chr7:128312406-128312456	HRCEpiC	kidney:	n/a
21	chr7:128312406-128312456	Jurkat	blood:	n/a
22	chr7:128312406-128312456	ECC-1	luminal epithelium:	n/a
23	chr7:128312406-128312456	MCF-7	breast:	n/a
24	chr7:128312406-128312456	SK-N-SH_RA	brain:	n/a
25	chr7:128312406-128312456	BE2_C	brain:	n/a
26	chr7:128312406-128312456	GM12878	blood:	n/a
27	chr7:128312406-128312456	AG10803	skin:	n/a
28	chr7:128312406-128312456	GM12892	blood:	n/a
29	chr7:128312406-128312456	SAEC	small airway:	n/a
30	chr7:128312406-128312456	PANC-1	pancreas:	n/a
31	chr7:128312406-128312456	A549	lung:	n/a
32	chr7:128312406-128312456	HAEpiC	amniotic membrane:	n/a
33	chr7:128312406-128312456	HPAEpiC	pulmonary alveolar:	n/a
34	chr7:128312406-128312456	IMR90	lung:	fetal
35	chr7:128312406-128312456	NHDF-neo	bronchial:	n/a
36	chr7:128312406-128312456	HCT-116	colon:	n/a
37	chr7:128312406-128312456	T-47D	breast:	n/a
38	chr7:128312406-128312456	HIPEpiC	eye:	n/a
39	chr7:128312406-128312456	ovcar-3	ovarian:	n/a
40	chr7:128312406-128312456	GM06990	blood:	n/a
41	chr7:128312406-128312456	U87	brain:	n/a
42	chr7:128312406-128312456	SK-N-SH	brain:	n/a
43	chr7:128312406-128312456	RPTEC	kidney:	n/a
44	chr7:128312406-128312456	K562	blood:	n/a
45	chr7:128312406-128312456	HCPEpiC	choroid plexus:	n/a
46	chr7:128312406-128312456	GM12891	blood:	n/a
47	chr7:128312406-128312456	HepG2	liver:	n/a
48	chr7:128312406-128312456	BJ	skin:	n/a
49	chr7:128312406-128312456	HCF	heart:	n/a
50	chr7:128312406-128312456	AG09319	gingival:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:128311065..128312727-chr7:128337751..128339462,2	K562	blood:
2	chr7:128311765..128313824-chr7:128325788..128328720,2	K562	blood:
3	chr7:128306825..128310882-chr7:128311566..128316462,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000241493	TF binding region
ENSG00000241493	CpG island
ENSG00000241493	Chromatin interaction
ENSG00000271553	Chromatin interaction
ENSG00000270810	Chromatin interaction
ENSG00000252866	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1013514	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs101721	0.85[CHB][hapmap]
rs10488628	0.85[CHB][hapmap]
rs10954206	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11982488	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11983903	0.84[ASN][1000 genomes]
rs2956682	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4731481	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4731494	0.81[ASN][1000 genomes]
rs55817807	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55928948	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59287454	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60382581	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61437980	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62481896	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62481928	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62483311	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62483370	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6467200	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6467202	0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs6467203	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs6955870	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6965333	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6979304	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs6979575	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs7800335	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9768325	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:28)

SNP	Gene	Cis/trans	Tissue	Source
rs11769769	RP11-274B21.2	cis	Thyroid	GTEx
rs11769769	RP11-274B21.2	cis	Adipose Subcutaneous	GTEx
rs11769769	RP11-274B21.4	cis	Esophagus Mucosa	GTEx
rs11769769	RP11-274B21.2	cis	Stomach	GTEx
rs11769769	RP11-274B21.1	cis	Adipose Subcutaneous	GTEx
rs11769769	RP11-274B21.2	cis	Nerve Tibial	GTEx
rs11769769	TMEM209	cis	parietal	SCAN
rs11769769	TSGA14	cis	cerebellum	SCAN
rs11769769	CICP14	cis	Thyroid	GTEx
rs11769769	RP11-274B21.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11769769	RP11-274B21.1	cis	lung	GTEx
rs11769769	RP11-274B21.2	cis	Muscle Skeletal	GTEx
rs11769769	RP11-274B21.4	cis	Skin Sun Exposed Lower leg	GTEx
rs11769769	RP11-274B21.3	cis	Nerve Tibial	GTEx
rs11769769	C7orf54	cis	cerebellum	SCAN
rs11769769	RP11-274B21.3	cis	Thyroid	GTEx
rs11769769	RP11-274B21.4	cis	Adipose Subcutaneous	GTEx
rs11769769	RP11-274B21.4	cis	Stomach	GTEx
rs11769769	RP11-274B21.4	cis	lung	GTEx
rs11769769	RP11-274B21.4	cis	Thyroid	GTEx
rs11769769	RP11-274B21.2	cis	lung	GTEx
rs11769769	RP11-274B21.4	cis	Muscle Skeletal	GTEx
rs11769769	RP11-274B21.1	cis	Nerve Tibial	GTEx
rs11769769	CICP14	cis	Skin Sun Exposed Lower leg	GTEx
rs11769769	RP11-274B21.3	cis	Muscle Skeletal	GTEx
rs11769769	RP11-274B21.1	cis	Skin Sun Exposed Lower leg	GTEx
rs11769769	CICP14	cis	Artery Tibial	GTEx
rs11769769	RP11-274B21.4	cis	Nerve Tibial	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128249600-128319600	Weak transcription	NHLF	lung
2	chr7:128284200-128313200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr7:128284400-128313200	Weak transcription	Colon Smooth Muscle	Colon
4	chr7:128294000-128313200	Weak transcription	Brain Germinal Matrix	brain
5	chr7:128294800-128328000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:128295000-128319800	Weak transcription	Left Ventricle	heart
7	chr7:128295000-128319800	Weak transcription	Right Ventricle	heart
8	chr7:128295000-128325200	Weak transcription	Brain Hippocampus Middle	brain
9	chr7:128295400-128325400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:128298600-128329200	Weak transcription	Pancreas	Pancrea
11	chr7:128300200-128313200	Weak transcription	Right Atrium	heart
12	chr7:128302200-128318200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr7:128302400-128319800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr7:128302400-128323200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:128302400-128323200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr7:128302400-128324000	Weak transcription	Aorta	Aorta
17	chr7:128302400-128337200	Weak transcription	Gastric	stomach
18	chr7:128302600-128312800	Weak transcription	Fetal Stomach	stomach
19	chr7:128302600-128323000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr7:128302600-128327800	Weak transcription	Placenta	Placenta
21	chr7:128302800-128321800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr7:128303000-128312800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr7:128303600-128319400	Weak transcription	Fetal Brain Female	brain
24	chr7:128305000-128323000	Weak transcription	NHDF-Ad	bronchial
25	chr7:128305400-128317600	Weak transcription	Osteobl	bone
26	chr7:128307200-128313000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:128308400-128323800	Weak transcription	A549	lung
28	chr7:128309000-128323000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:128310000-128319600	Weak transcription	Adipose Nuclei	Adipose
30	chr7:128310000-128329400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr7:128310600-128323200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr7:128311000-128313200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr7:128311200-128318400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr7:128311200-128319400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:128311200-128327000	Weak transcription	HSMM	muscle
36	chr7:128311400-128313000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:128311600-128327800	Weak transcription	Brain Substantia Nigra	brain
38	chr7:128311800-128313400	Enhancers	Stomach Smooth Muscle	stomach
39	chr7:128312000-128312600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:128312000-128313400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr7:128312000-128313400	Enhancers	Fetal Muscle Leg	muscle
42	chr7:128312000-128313400	Enhancers	Lung	lung
43	chr7:128312200-128313800	Enhancers	Psoas Muscle	Psoas
44	chr7:128312200-128318200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr7:128312200-128322800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr7:128312400-128312600	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr7:128312400-128313200	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr7:128312400-128325400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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