Variant report

Variant	rs73995917
Chromosome Location	chr2:234261175-234261176
allele	C/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:4)
LncRNA
region (count:2)
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	chr2:234261155-234261205	HCT-116	colon:	n/a
2	chr2:234261155-234261205	HPAEpiC	pulmonary alveolar:	n/a
3	chr2:234261155-234261205	Caco-2	colon:	n/a
4	chr2:234261155-234261205	HRE	kidney:	n/a
5	chr2:234261155-234261205	MCF-7	breast:	n/a
6	chr2:234261155-234261205	SK-N-MC	brain:	n/a
7	chr2:234261155-234261205	ProgFib	skin:	n/a
8	chr2:234261155-234261205	GM19239	blood:	n/a
9	chr2:234261155-234261205	IMR90	lung:	fetal
10	chr2:234261155-234261205	BE2_C	brain:	n/a
11	chr2:234261155-234261205	HCF	heart:	n/a
12	chr2:234261155-234261205	RPTEC	kidney:	n/a
13	chr2:234261155-234261205	GM12891	blood:	n/a
14	chr2:234261155-234261205	H1-hESC	embryonic stem cell:	embryo
15	chr2:234261155-234261205	AG04450	lung:	fetal
16	chr2:234261155-234261205	ovcar-3	ovarian:	n/a
17	chr2:234261155-234261205	HAEpiC	amniotic membrane:	n/a
18	chr2:234261155-234261205	HEK293	kidney:	embryo
19	chr2:234261155-234261205	A549	lung:	n/a
20	chr2:234261155-234261205	HEEpiC	esophagus:	n/a
21	chr2:234261155-234261205	HIPEpiC	eye:	n/a
22	chr2:234261155-234261205	LNCaP	prostate:	n/a
23	chr2:234261155-234261205	SAEC	small airway:	n/a
24	chr2:234261155-234261205	Hepatocyte	liver:	n/a
25	chr2:234261155-234261205	Jurkat	blood:	n/a
26	chr2:234261155-234261205	AG09309	skin:	n/a
27	chr2:234261155-234261205	NH-A	brain:	n/a
28	chr2:234261155-234261205	HRPEpiC	eye:	n/a
29	chr2:234261155-234261205	AG10803	skin:	n/a
30	chr2:234261155-234261205	PFSK-1	brain:	n/a
31	chr2:234261155-234261205	AoSMC	blood vessel:	n/a
32	chr2:234261155-234261205	NB4	blood:	n/a
33	chr2:234261155-234261205	AG09319	gingival:	n/a
34	chr2:234261155-234261205	HCM	heart:	n/a
35	chr2:234261155-234261205	CMK	blood:	n/a
36	chr2:234261155-234261205	NHBE	bronchial:	n/a
37	chr2:234261155-234261205	BJ	skin:	n/a
38	chr2:234261155-234261205	GM06990	blood:	n/a
39	chr2:234261155-234261205	HepG2	liver:	n/a
40	chr2:234261155-234261205	HMEC	breast:	n/a
41	chr2:234261155-234261205	U87	brain:	n/a
42	chr2:234261155-234261205	HRCEpiC	kidney:	n/a
43	chr2:234261155-234261205	PrEC	prostate:	n/a
44	chr2:234261155-234261205	GM12878	blood:	n/a
45	chr2:234261155-234261205	SK-N-SH_RA	brain:	n/a
46	chr2:234261155-234261205	GM12892	blood:	n/a
47	chr2:234261155-234261205	T-47D	breast:	n/a
48	chr2:234261155-234261205	MCF10A-Er-Src	breast:	n/a
49	chr2:234261155-234261205	AG04449	skin:	fetal
50	chr2:234261155-234261205	SK-N-SH	brain:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:234260930..234263276-chr20:55839671..55841991,2	MCF-7	breast:
2	chr2:234252596..234255070-chr2:234259544..234261790,2	MCF-7	breast:
3	chr2:234250454..234252817-chr2:234259507..234261649,2	MCF-7	breast:
4	chr2:234259434..234265610-chr2:234290886..234296562,9	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP40-1	chr2:234259778-234262062	ENSG00000259793.1
2	lnc-USP40-1	chr2:234260441-234262062	NONHSAT077479

No data

Variant related genes	Relation type
DGKD	CpG island
ENSG00000243637	CpG island
ENSG00000101144	Chromatin interaction
ENSG00000077044	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000130561	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs59125245	0.90[AFR][1000 genomes]
rs6431327	0.84[AFR][1000 genomes]
rs73995910	0.89[AFR][1000 genomes]
rs7588587	0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1002075	chr2:234225979-234277508	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv460135	chr2:234242347-234288048	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv584701	chr2:234242347-234288048	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv460136	chr2:234244395-234288048	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv584702	chr2:234244395-234288048	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234255800-234262400	Weak transcription	Right Atrium	heart
2	chr2:234256400-234262400	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr2:234256600-234261400	Enhancers	Primary B cells from cord blood	blood
4	chr2:234256800-234262400	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr2:234257000-234262200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr2:234257800-234263000	Enhancers	Placenta Amnion	Placenta Amnion
7	chr2:234258000-234261800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:234258200-234261200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr2:234258200-234261800	Weak transcription	Esophagus	oesophagus
10	chr2:234258200-234261800	Weak transcription	Lung	lung
11	chr2:234258200-234262000	Weak transcription	Right Ventricle	heart
12	chr2:234258200-234262600	Weak transcription	Psoas Muscle	Psoas
13	chr2:234258400-234261800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:234258400-234261800	Weak transcription	Gastric	stomach
15	chr2:234258400-234261800	Weak transcription	Thymus	Thymus
16	chr2:234258400-234262000	Enhancers	Duodenum Mucosa	Duodenum
17	chr2:234258400-234262200	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr2:234258400-234262400	Weak transcription	Ovary	ovary
19	chr2:234258600-234261400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr2:234258600-234261800	Weak transcription	Spleen	Spleen
21	chr2:234258600-234262000	Weak transcription	Adipose Nuclei	Adipose
22	chr2:234258600-234262000	Weak transcription	Brain Substantia Nigra	brain
23	chr2:234258600-234262200	Weak transcription	Primary T cells from cord blood	blood
24	chr2:234258600-234262400	Weak transcription	Fetal Kidney	kidney
25	chr2:234258800-234262600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:234259200-234261800	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:234259200-234262400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:234259400-234261800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr2:234259400-234262400	Weak transcription	Brain Angular Gyrus	brain
30	chr2:234259400-234263200	Weak transcription	Small Intestine	intestine
31	chr2:234259600-234261200	Weak transcription	GM12878-XiMat	blood
32	chr2:234259600-234261600	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:234259600-234261600	Weak transcription	Colonic Mucosa	Colon
34	chr2:234259600-234262200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:234259800-234261200	Weak transcription	Placenta	Placenta
36	chr2:234259800-234261600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr2:234259800-234261800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr2:234259800-234262000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:234259800-234262000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:234259800-234262200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:234259800-234262400	Weak transcription	HSMMtube	muscle
42	chr2:234259800-234262400	Weak transcription	NHLF	lung
43	chr2:234260000-234261600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr2:234260000-234261600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr2:234260000-234261600	Weak transcription	Stomach Mucosa	stomach
46	chr2:234260000-234261800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr2:234260000-234261800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:234260000-234262200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr2:234260000-234262200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:234260200-234261600	Weak transcription	HepG2	liver

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