Variant report

Variant	rs254206
Chromosome Location	chr5:115895195-115895196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr5:115894860-115895251	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr5:115894781-115896063	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:115894958-115895282	H1-hESC	embryonic stem cell:	n/a	n/a
4	SP1	chr5:115894875-115895305	H1-hESC	embryonic stem cell:	n/a	n/a
5	SIN3AK20	chr5:115894892-115895199	H1-hESC	embryonic stem cell:	n/a	n/a
6	YY1	chr5:115894863-115895881	H1-hESC	embryonic stem cell:	n/a	n/a
7	TCF12	chr5:115894830-115895242	H1-hESC	embryonic stem cell:	n/a	n/a
8	TCF12	chr5:115894868-115895213	H1-hESC	embryonic stem cell:	n/a	n/a
9	SETDB1	chr5:115895108-115895493	U2OS	brain:	n/a	n/a
10	TBP	chr5:115894930-115895247	H1-hESC	embryonic stem cell:	n/a	n/a
11	ELF1	chr5:115894906-115895363	GM12878	blood:	n/a	n/a
12	POLR2A	chr5:115894489-115896585	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr5:115894807-115895947	H1-hESC	embryonic stem cell:	n/a	n/a
14	SIN3A	chr5:115894845-115895458	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr5:115894797-115895296	H1-hESC	embryonic stem cell:	n/a	n/a
16	YY1	chr5:115894905-115895410	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115895001..115897524-chr5:115899186..115901085,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000239528	TF binding region
SEMA6A	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs153638	0.86[ASN][1000 genomes]
rs153640	0.88[ASN][1000 genomes]
rs153641	0.89[ASN][1000 genomes]
rs17140144	0.83[ASN][1000 genomes]
rs254076	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs254077	0.89[ASN][1000 genomes]
rs254080	0.89[ASN][1000 genomes]
rs254207	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs254208	0.96[ASN][1000 genomes]
rs254209	0.96[ASN][1000 genomes]
rs254210	0.94[ASN][1000 genomes]
rs254226	0.88[ASN][1000 genomes]
rs254227	0.82[ASN][1000 genomes]
rs254229	0.82[ASN][1000 genomes]
rs254234	0.85[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	esv3357229	chr5:115893403-115895551	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115880800-115900600	Weak transcription	Fetal Kidney	kidney
2	chr5:115882600-115895400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:115886600-115901000	Weak transcription	Placenta	Placenta
4	chr5:115887400-115897000	Weak transcription	Small Intestine	intestine
5	chr5:115889000-115895200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr5:115889400-115899400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:115889600-115895400	Weak transcription	Fetal Brain Female	brain
8	chr5:115889600-115898400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:115890000-115900800	Enhancers	Brain Hippocampus Middle	brain
10	chr5:115890600-115907800	Weak transcription	Spleen	Spleen
11	chr5:115890800-115895600	Weak transcription	Pancreas	Pancrea
12	chr5:115890800-115895800	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:115890800-115898800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:115890800-115907600	Weak transcription	Colonic Mucosa	Colon
15	chr5:115891000-115895800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr5:115891000-115898200	Weak transcription	Right Atrium	heart
17	chr5:115891000-115900600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:115891000-115907600	Weak transcription	Ovary	ovary
19	chr5:115891200-115904600	Weak transcription	Fetal Stomach	stomach
20	chr5:115891400-115895400	Weak transcription	Psoas Muscle	Psoas
21	chr5:115891400-115905200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:115893200-115895200	Weak transcription	Fetal Muscle Leg	muscle
23	chr5:115893200-115895400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:115893400-115895600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:115893600-115895400	Weak transcription	HepG2	liver
26	chr5:115893600-115895600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr5:115893600-115896400	Weak transcription	Fetal Intestine Large	intestine
28	chr5:115893800-115902400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr5:115894400-115895200	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr5:115894400-115897000	Enhancers	Primary hematopoietic stem cells	blood
31	chr5:115894400-115900800	Enhancers	Brain Cingulate Gyrus	brain
32	chr5:115894400-115902600	Enhancers	Brain Substantia Nigra	brain
33	chr5:115894600-115895600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr5:115894600-115896000	Enhancers	Brain Anterior Caudate	brain
35	chr5:115894600-115896400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr5:115894600-115896400	Enhancers	Brain Angular Gyrus	brain
37	chr5:115894600-115896600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:115894600-115896600	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr5:115894600-115897200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr5:115894600-115897400	Enhancers	H1 Cell Line	embryonic stem cell
41	chr5:115894600-115897600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr5:115894800-115895200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:115894800-115895400	Enhancers	Primary B cells from peripheral blood	blood
44	chr5:115894800-115895600	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr5:115894800-115895800	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr5:115894800-115896000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr5:115894800-115896000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr5:115894800-115896000	Strong transcription	Fetal Intestine Small	intestine
49	chr5:115894800-115896400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:115894800-115896600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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