Variant report

Variant	rs1341316
Chromosome Location	chr1:58087789-58087790
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10789052	0.89[CHB][hapmap]
rs10889059	0.84[CHB][hapmap];0.87[CHD][hapmap];0.88[MEX][hapmap]
rs10889061	0.84[CHB][hapmap];0.87[CHD][hapmap];0.83[MEX][hapmap]
rs11207075	0.82[CHB][hapmap]
rs11207080	0.86[CHD][hapmap];0.88[MEX][hapmap]
rs11207088	0.82[CHB][hapmap]
rs11800684	0.92[CHB][hapmap];0.91[CHD][hapmap]
rs11801131	0.92[CHB][hapmap];0.91[CHD][hapmap];0.83[MEX][hapmap]
rs11809742	0.84[CHB][hapmap];0.81[YRI][hapmap]
rs12120378	0.92[CHB][hapmap];0.81[YRI][hapmap]
rs12123728	0.92[CHB][hapmap];0.91[CHD][hapmap];0.83[MEX][hapmap];0.81[YRI][hapmap]
rs12124076	0.92[CHB][hapmap]
rs12125360	0.92[CHB][hapmap];0.81[YRI][hapmap]
rs12125452	0.92[CHB][hapmap]
rs12127845	0.92[CHB][hapmap]
rs12133913	0.84[CHB][hapmap]
rs2103142	0.91[CHB][hapmap]
rs4076379	0.84[CHB][hapmap]
rs4244010	0.84[CHB][hapmap]
rs4484949	0.92[CHB][hapmap];0.91[CHD][hapmap]
rs6675237	0.92[CHB][hapmap]
rs6687594	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7339963	0.92[CHB][hapmap];0.87[CHD][hapmap];0.83[MEX][hapmap]
rs7522826	0.92[CHB][hapmap];0.82[CHD][hapmap];0.88[MEX][hapmap]
rs7532516	0.92[CHB][hapmap]
rs7554762	0.92[CHB][hapmap]
rs7554847	0.92[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1012555	chr1:57950355-58103389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv523574	chr1:58018103-58087789	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv871684	chr1:58021206-58096379	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1341316	TACSTD2	cis	cerebellum	SCAN
rs1341316	TMEM59	cis	cerebellum	SCAN
rs1341316	C1orf175	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58066000-58089000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:58066400-58089400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:58081200-58090600	Enhancers	Fetal Heart	heart
4	chr1:58081600-58089800	Enhancers	Fetal Muscle Leg	muscle
5	chr1:58083400-58088800	Weak transcription	HSMMtube	muscle
6	chr1:58085400-58093600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:58086200-58089800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr1:58086400-58088200	Weak transcription	Fetal Lung	lung
9	chr1:58086400-58089600	Enhancers	Fetal Brain Male	brain
10	chr1:58086600-58088400	Weak transcription	Fetal Brain Female	brain
11	chr1:58086800-58087800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:58086800-58088200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:58086800-58088400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:58086800-58088600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:58086800-58088600	Weak transcription	Right Atrium	heart
16	chr1:58086800-58088800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:58086800-58088800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:58086800-58088800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:58086800-58088800	Weak transcription	Left Ventricle	heart
20	chr1:58086800-58088800	Weak transcription	HepG2	liver
21	chr1:58087000-58088200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:58087000-58088200	Weak transcription	Fetal Kidney	kidney
23	chr1:58087000-58088400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:58087000-58088400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:58087000-58088800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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