Variant report

Variant	rs153641
Chromosome Location	chr5:115891789-115891790
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs153638	0.96[ASN][1000 genomes]
rs153640	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	1.00[ASN][1000 genomes]
rs254077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs254080	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs254081	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs254206	0.89[ASN][1000 genomes]
rs254207	0.89[ASN][1000 genomes]
rs254208	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]
rs254209	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs254210	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs254226	1.00[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs254227	1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs254229	1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs254233	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs254234	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs153641	SEMA6A	cis	cerebellum	SCAN

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	chr5:115886600-115892200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr5:115886600-115901000	Weak transcription	Placenta	Placenta
10	chr5:115887400-115895000	Weak transcription	Lung	lung
11	chr5:115887400-115897000	Weak transcription	Small Intestine	intestine
12	chr5:115888400-115893800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:115889000-115895200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr5:115889200-115891800	Enhancers	H9 Cell Line	embryonic stem cell
15	chr5:115889200-115892600	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr5:115889200-115893600	Enhancers	Brain Substantia Nigra	brain
17	chr5:115889400-115893000	Enhancers	Fetal Intestine Small	intestine
18	chr5:115889400-115895000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:115889400-115899400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:115889600-115895400	Weak transcription	Fetal Brain Female	brain
21	chr5:115889600-115898400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:115890000-115893400	Enhancers	Brain Angular Gyrus	brain
23	chr5:115890000-115900800	Enhancers	Brain Hippocampus Middle	brain
24	chr5:115890200-115893200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr5:115890400-115893000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:115890400-115893600	Enhancers	HepG2	liver
27	chr5:115890600-115893800	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr5:115890600-115907800	Weak transcription	Spleen	Spleen
29	chr5:115890800-115894800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:115890800-115894800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:115890800-115894800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr5:115890800-115895000	Weak transcription	Left Ventricle	heart
33	chr5:115890800-115895600	Weak transcription	Pancreas	Pancrea
34	chr5:115890800-115895800	Weak transcription	Colon Smooth Muscle	Colon
35	chr5:115890800-115898800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr5:115890800-115907600	Weak transcription	Colonic Mucosa	Colon
37	chr5:115891000-115891800	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr5:115891000-115892000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr5:115891000-115892400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
40	chr5:115891000-115892800	Weak transcription	Fetal Muscle Leg	muscle
41	chr5:115891000-115894200	Enhancers	Brain Anterior Caudate	brain
42	chr5:115891000-115894600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr5:115891000-115894600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr5:115891000-115894600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:115891000-115895800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr5:115891000-115898200	Weak transcription	Right Atrium	heart
47	chr5:115891000-115900600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:115891000-115907600	Weak transcription	Ovary	ovary
49	chr5:115891200-115892200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr5:115891200-115892600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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