Variant report

Variant	rs254208
Chromosome Location	chr5:115894895-115894896
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	SP1	chr5:115894875-115895305	H1-hESC	embryonic stem cell:	n/a	n/a
4	SIN3AK20	chr5:115894892-115895199	H1-hESC	embryonic stem cell:	n/a	n/a
5	YY1	chr5:115894863-115895881	H1-hESC	embryonic stem cell:	n/a	n/a
6	TCF12	chr5:115894830-115895242	H1-hESC	embryonic stem cell:	n/a	n/a
7	ATF2	chr5:115894735-115895142	H1-hESC	embryonic stem cell:	n/a	n/a
8	TCF12	chr5:115894868-115895213	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr5:115894489-115896585	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr5:115894807-115895947	H1-hESC	embryonic stem cell:	n/a	n/a
11	SIN3A	chr5:115894845-115895458	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr5:115894797-115895296	H1-hESC	embryonic stem cell:	n/a	n/a

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

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs153638	0.90[ASN][1000 genomes]
rs153640	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs153641	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs254076	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs254077	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs254080	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs254081	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs254206	0.96[ASN][1000 genomes]
rs254207	0.96[ASN][1000 genomes]
rs254209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs254210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs254226	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs254227	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs254229	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs254233	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs254234	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv3420287	chr5:115893903-115895001	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 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	chr5:115887400-115895000	Weak transcription	Lung	lung
5	chr5:115887400-115897000	Weak transcription	Small Intestine	intestine
6	chr5:115889000-115895200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr5:115889400-115895000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:115889400-115899400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:115889600-115895400	Weak transcription	Fetal Brain Female	brain
10	chr5:115889600-115898400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:115890000-115900800	Enhancers	Brain Hippocampus Middle	brain
12	chr5:115890600-115907800	Weak transcription	Spleen	Spleen
13	chr5:115890800-115895000	Weak transcription	Left Ventricle	heart
14	chr5:115890800-115895600	Weak transcription	Pancreas	Pancrea
15	chr5:115890800-115895800	Weak transcription	Colon Smooth Muscle	Colon
16	chr5:115890800-115898800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:115890800-115907600	Weak transcription	Colonic Mucosa	Colon
18	chr5:115891000-115895800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:115891000-115898200	Weak transcription	Right Atrium	heart
20	chr5:115891000-115900600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:115891000-115907600	Weak transcription	Ovary	ovary
22	chr5:115891200-115904600	Weak transcription	Fetal Stomach	stomach
23	chr5:115891400-115895400	Weak transcription	Psoas Muscle	Psoas
24	chr5:115891400-115905200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:115893200-115895000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr5:115893200-115895200	Weak transcription	Fetal Muscle Leg	muscle
27	chr5:115893200-115895400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:115893400-115895000	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr5:115893400-115895600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:115893600-115895000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr5:115893600-115895400	Weak transcription	HepG2	liver
32	chr5:115893600-115895600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr5:115893600-115896400	Weak transcription	Fetal Intestine Large	intestine
34	chr5:115893800-115902400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr5:115894400-115895200	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr5:115894400-115897000	Enhancers	Primary hematopoietic stem cells	blood
37	chr5:115894400-115900800	Enhancers	Brain Cingulate Gyrus	brain
38	chr5:115894400-115902600	Enhancers	Brain Substantia Nigra	brain
39	chr5:115894600-115895000	Enhancers	H9 Cell Line	embryonic stem cell
40	chr5:115894600-115895600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr5:115894600-115896000	Enhancers	Brain Anterior Caudate	brain
42	chr5:115894600-115896400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr5:115894600-115896400	Enhancers	Brain Angular Gyrus	brain
44	chr5:115894600-115896600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:115894600-115896600	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr5:115894600-115897200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr5:115894600-115897400	Enhancers	H1 Cell Line	embryonic stem cell
48	chr5:115894600-115897600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr5:115894800-115895000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr5:115894800-115895200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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