Variant report

Variant	rs153640
Chromosome Location	chr5:115892410-115892411
allele	A/C
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	POLR2A	chr5:115892189-115892853	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115873178..115874811-chr5:115890679..115892572,2	K562	blood:

Variant related genes	Relation type
SEMA6A	TF binding region

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

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

rs_ID	r²[population]
rs153638	0.98[ASN][1000 genomes]
rs153641	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs254076	0.99[ASN][1000 genomes]
rs254077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[ASN][1000 genomes]
rs254080	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[ASN][1000 genomes]
rs254081	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs254206	0.88[ASN][1000 genomes]
rs254207	0.88[ASN][1000 genomes]
rs254208	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]
rs254209	0.88[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs254210	0.88[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs254226	1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs254227	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs254229	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs254233	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs254234	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[ASN][1000 genomes]

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115878200-115893200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr5:115880800-115900600	Weak transcription	Fetal Kidney	kidney
3	chr5:115882600-115895400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr5:115884800-115893200	Enhancers	Brain Cingulate Gyrus	brain
5	chr5:115885400-115894000	Genic enhancers	HUES64 Cell Line	embryonic stem cell
6	chr5:115885400-115894600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr5:115885800-115893600	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr5:115886600-115901000	Weak transcription	Placenta	Placenta
9	chr5:115887400-115895000	Weak transcription	Lung	lung
10	chr5:115887400-115897000	Weak transcription	Small Intestine	intestine
11	chr5:115888400-115893800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:115889000-115895200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr5:115889200-115892600	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr5:115889200-115893600	Enhancers	Brain Substantia Nigra	brain
15	chr5:115889400-115893000	Enhancers	Fetal Intestine Small	intestine
16	chr5:115889400-115895000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr5:115889400-115899400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:115889600-115895400	Weak transcription	Fetal Brain Female	brain
19	chr5:115889600-115898400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:115890000-115893400	Enhancers	Brain Angular Gyrus	brain
21	chr5:115890000-115900800	Enhancers	Brain Hippocampus Middle	brain
22	chr5:115890200-115893200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr5:115890400-115893000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:115890400-115893600	Enhancers	HepG2	liver
25	chr5:115890600-115893800	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr5:115890600-115907800	Weak transcription	Spleen	Spleen
27	chr5:115890800-115894800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:115890800-115894800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:115890800-115894800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr5:115890800-115895000	Weak transcription	Left Ventricle	heart
31	chr5:115890800-115895600	Weak transcription	Pancreas	Pancrea
32	chr5:115890800-115895800	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:115890800-115898800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr5:115890800-115907600	Weak transcription	Colonic Mucosa	Colon
35	chr5:115891000-115892800	Weak transcription	Fetal Muscle Leg	muscle
36	chr5:115891000-115894200	Enhancers	Brain Anterior Caudate	brain
37	chr5:115891000-115894600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr5:115891000-115894600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr5:115891000-115894600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:115891000-115895800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr5:115891000-115898200	Weak transcription	Right Atrium	heart
42	chr5:115891000-115900600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:115891000-115907600	Weak transcription	Ovary	ovary
44	chr5:115891200-115892600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:115891200-115904600	Weak transcription	Fetal Stomach	stomach
46	chr5:115891400-115893000	Weak transcription	Fetal Intestine Large	intestine
47	chr5:115891400-115895400	Weak transcription	Psoas Muscle	Psoas
48	chr5:115891400-115905200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr5:115891600-115893000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr5:115891800-115894600	Weak transcription	H9 Cell Line	embryonic stem cell

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