Variant report

Variant	rs61060916
Chromosome Location	chr17:17908127-17908128
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:17908120-17908270	HAc	cerebellar:	n/a	n/a
2	CTCF	chr17:17908000-17908150	HBMEC	blood vessel:	n/a	n/a
3	REST	chr17:17907524-17908962	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr17:17907983-17908678	H1-neurons	neurons:	n/a	n/a
5	CTCF	chr17:17908024-17908893	A549	lung:	n/a	n/a
6	POLR2A	chr17:17907594-17908693	H1-neurons	neurons:	n/a	n/a
7	REST	chr17:17907991-17908597	H1-neurons	neurons:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:17908098-17908148	Hepatocyte	liver:	n/a
2	chr17:17908098-17908148	SK-N-MC	brain:	n/a
3	chr17:17908098-17908148	GM06990	blood:	n/a
4	chr17:17908098-17908148	SK-N-SH_RA	brain:	n/a
5	chr17:17908098-17908148	K562	blood:	n/a
6	chr17:17908098-17908148	AoSMC	blood vessel:	n/a
7	chr17:17908098-17908148	AG09319	gingival:	n/a
8	chr17:17908098-17908148	HEEpiC	esophagus:	n/a
9	chr17:17908098-17908148	CMK	blood:	n/a
10	chr17:17908098-17908148	HL-60	blood:	n/a
11	chr17:17908098-17908148	PANC-1	pancreas:	n/a
12	chr17:17908098-17908148	NHDF-neo	bronchial:	n/a
13	chr17:17908098-17908148	Hela-S3	cervix:	n/a
14	chr17:17908098-17908148	PFSK-1	brain:	n/a
15	chr17:17908098-17908148	SK-N-SH	brain:	n/a
16	chr17:17908098-17908148	NT2-D1	testis:	n/a
17	chr17:17908098-17908148	ECC-1	luminal epithelium:	n/a
18	chr17:17908098-17908148	AG10803	skin:	n/a
19	chr17:17908098-17908148	NH-A	brain:	n/a
20	chr17:17908098-17908148	HAEpiC	amniotic membrane:	n/a
21	chr17:17908098-17908148	SKMC	muscle:	n/a
22	chr17:17908098-17908148	HRCEpiC	kidney:	n/a
23	chr17:17908098-17908148	SAEC	small airway:	n/a
24	chr17:17908098-17908148	NB4	blood:	n/a
25	chr17:17908098-17908148	GM19239	blood:	n/a
26	chr17:17908098-17908148	U87	brain:	n/a
27	chr17:17908098-17908148	PrEC	prostate:	n/a
28	chr17:17908098-17908148	T-47D	breast:	n/a
29	chr17:17908098-17908148	HRE	kidney:	n/a
30	chr17:17908098-17908148	HCM	heart:	n/a
31	chr17:17908098-17908148	HepG2	liver:	n/a
32	chr17:17908098-17908148	H1-hESC	embryonic stem cell:	embryo
33	chr17:17908098-17908148	HUVEC	blood vessel:	n/a
34	chr17:17908098-17908148	BJ	skin:	n/a
35	chr17:17908098-17908148	NHBE	bronchial:	n/a
36	chr17:17908098-17908148	MCF10A-Er-Src	breast:	n/a
37	chr17:17908098-17908148	HCPEpiC	choroid plexus:	n/a
38	chr17:17908098-17908148	HMEC	breast:	n/a
39	chr17:17908098-17908148	HCT-116	colon:	n/a
40	chr17:17908098-17908148	A549	lung:	n/a
41	chr17:17908098-17908148	ProgFib	skin:	n/a
42	chr17:17908098-17908148	GM12878	blood:	n/a
43	chr17:17908098-17908148	GM12891	blood:	n/a
44	chr17:17908098-17908148	AG04450	lung:	fetal
45	chr17:17908098-17908148	HCF	heart:	n/a
46	chr17:17908098-17908148	AG09309	skin:	n/a
47	chr17:17908098-17908148	IMR90	lung:	fetal
48	chr17:17908098-17908148	HNPCEpiC	eye:	n/a
49	chr17:17908098-17908148	BE2_C	brain:	n/a
50	chr17:17908098-17908148	GM12892	blood:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr17:17903006..17906615-chr17:17908063..17910293,3	K562	blood:
2	chr17:17904155..17906615-chr17:17908063..17910293,2	K562	blood:
3	chr17:17901247..17903124-chr17:17907149..17909889,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATPAF2-1	chr17:17907231-17909643	NONHSAT146130

No data

Variant related genes	Relation type
LRRC48	TF binding region
ENSG00000201378	TF binding region
LRRC48	CpG island
ENSG00000201378	CpG island
ENSG00000201378	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs16960767	1.00[AMR][1000 genomes]
rs16960818	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56054716	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56153053	1.00[AMR][1000 genomes]
rs56160247	1.00[AMR][1000 genomes]
rs56232485	1.00[AMR][1000 genomes]
rs56928492	1.00[AMR][1000 genomes]
rs57082481	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57277459	1.00[AMR][1000 genomes]
rs57791826	1.00[AMR][1000 genomes]
rs58219643	1.00[AMR][1000 genomes]
rs58376085	1.00[AMR][1000 genomes]
rs58676524	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58936409	1.00[AMR][1000 genomes]
rs61050785	1.00[AMR][1000 genomes]
rs61188141	1.00[AMR][1000 genomes]
rs61256737	1.00[AMR][1000 genomes]
rs7218054	1.00[AMR][1000 genomes]
rs7218246	1.00[AMR][1000 genomes]
rs7218594	1.00[AMR][1000 genomes]
rs7221934	1.00[AMR][1000 genomes]
rs7224621	1.00[AMR][1000 genomes]
rs73297834	1.00[AMR][1000 genomes]
rs73297855	1.00[AMR][1000 genomes]
rs73297868	1.00[AMR][1000 genomes]
rs73299861	1.00[AMR][1000 genomes]
rs73299873	1.00[AMR][1000 genomes]
rs73299892	1.00[AMR][1000 genomes]
rs73301827	1.00[AMR][1000 genomes]
rs73301859	1.00[AMR][1000 genomes]
rs73301894	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73303812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73303813	1.00[AMR][1000 genomes]
rs73303833	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73303854	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73303856	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73303857	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73305952	1.00[AMR][1000 genomes]
rs73979211	1.00[AMR][1000 genomes]
rs73979217	1.00[AMR][1000 genomes]
rs73979243	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73981076	1.00[AMR][1000 genomes]
rs8066528	1.00[AMR][1000 genomes]
rs8066865	1.00[AMR][1000 genomes]
rs8078368	1.00[AMR][1000 genomes]
rs8078811	1.00[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	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
5	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv510701	chr17:17850474-17955485	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17876600-17914600	Weak transcription	Aorta	Aorta
2	chr17:17876800-17909400	Weak transcription	Brain Substantia Nigra	brain
3	chr17:17876800-17912000	Weak transcription	Colon Smooth Muscle	Colon
4	chr17:17881800-17908200	Weak transcription	Pancreas	Pancrea
5	chr17:17886800-17909400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr17:17886800-17913000	Weak transcription	Fetal Lung	lung
7	chr17:17892200-17908400	Weak transcription	Lung	lung
8	chr17:17892400-17910800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr17:17892600-17909800	Weak transcription	Brain Angular Gyrus	brain
10	chr17:17894000-17920600	Weak transcription	Stomach Mucosa	stomach
11	chr17:17894600-17911400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr17:17895200-17909600	Weak transcription	NHLF	lung
13	chr17:17898000-17909200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr17:17898000-17910800	Weak transcription	Brain Hippocampus Middle	brain
15	chr17:17898200-17908200	Weak transcription	Right Ventricle	heart
16	chr17:17898200-17908400	Weak transcription	Fetal Brain Female	brain
17	chr17:17898200-17909000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr17:17898200-17918000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr17:17898200-17918000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr17:17898400-17910000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr17:17898400-17911400	Weak transcription	HSMM	muscle
22	chr17:17898600-17908400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr17:17898600-17909800	Weak transcription	Adipose Nuclei	Adipose
24	chr17:17898600-17909800	Weak transcription	Ovary	ovary
25	chr17:17898600-17910600	Weak transcription	Placenta	Placenta
26	chr17:17898600-17910800	Weak transcription	Esophagus	oesophagus
27	chr17:17898600-17917600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr17:17898800-17908800	Weak transcription	NHEK	skin
29	chr17:17901200-17908200	Weak transcription	Fetal Stomach	stomach
30	chr17:17901200-17909200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr17:17903000-17911400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr17:17903200-17909800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr17:17903400-17909600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr17:17903400-17909800	Weak transcription	Liver	Liver
35	chr17:17903600-17908800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr17:17903600-17913200	Weak transcription	Gastric	stomach
37	chr17:17903600-17913600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr17:17903800-17909800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr17:17904000-17910000	Weak transcription	Fetal Intestine Large	intestine
40	chr17:17904000-17911800	Weak transcription	HepG2	liver
41	chr17:17905000-17910800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr17:17905000-17912000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr17:17905800-17909600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr17:17905800-17909800	Weak transcription	Thymus	Thymus
45	chr17:17905800-17911400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr17:17906000-17908200	Weak transcription	Primary T cells from cord blood	blood
47	chr17:17906000-17911800	Weak transcription	NHDF-Ad	bronchial
48	chr17:17906000-17912000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr17:17906000-17914800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr17:17906200-17941400	Weak transcription	H9 Cell Line	embryonic stem cell

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