Variant report

Variant	rs11206973
Chromosome Location	chr1:57568923-57568924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10430117	0.85[ASN][1000 genomes]
rs11206971	0.89[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs11206972	0.80[EUR][1000 genomes]
rs12025887	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs12026247	0.81[JPT][hapmap]
rs12140416	0.81[JPT][hapmap]
rs12565535	0.87[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]
rs3729546	0.81[JPT][hapmap]
rs3738555	0.81[JPT][hapmap]
rs3738556	0.87[GIH][hapmap];0.82[JPT][hapmap]
rs3754260	1.00[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3754261	0.82[JPT][hapmap]
rs3754262	0.81[JPT][hapmap]
rs3754263	0.81[JPT][hapmap]
rs3768176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768177	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768184	0.92[CEU][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap]
rs3768187	0.92[CEU][hapmap]
rs3768192	0.87[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap]
rs3768194	0.87[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]
rs3820576	0.82[JPT][hapmap]
rs3820577	0.87[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap]
rs473562	0.82[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs514550	0.82[JPT][hapmap]
rs6587764	0.83[ASN][1000 genomes]
rs6660463	0.81[JPT][hapmap]
rs6669702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674223	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs960501	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11206973	SCP2	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57551400-57622000	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57565600-57569000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:57566600-57569400	Enhancers	H1 Cell Line	embryonic stem cell
4	chr1:57566600-57569400	Enhancers	Fetal Lung	lung
5	chr1:57566800-57569400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr1:57567000-57570800	Enhancers	Fetal Heart	heart
7	chr1:57567400-57576800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:57567600-57569000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:57567600-57570800	Weak transcription	Brain Germinal Matrix	brain
10	chr1:57568000-57569800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr1:57568200-57569200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr1:57568400-57569000	Enhancers	Fetal Stomach	stomach
13	chr1:57568400-57569200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr1:57568400-57569200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:57568400-57569200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:57568400-57569200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr1:57568400-57569200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr1:57568400-57569800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:57568400-57571200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:57568600-57569200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:57568600-57569200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr1:57568600-57569200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr1:57568600-57569400	Enhancers	Fetal Muscle Leg	muscle
24	chr1:57568600-57569400	Enhancers	Left Ventricle	heart
25	chr1:57568600-57569400	Enhancers	Ovary	ovary
26	chr1:57568800-57569200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr1:57568800-57569200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:57568800-57569200	Enhancers	Right Atrium	heart
29	chr1:57568800-57569400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:57568800-57569600	Enhancers	H9 Cell Line	embryonic stem cell
31	chr1:57568800-57569800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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