Variant report

Variant	rs1207881
Chromosome Location	chr7:78377750-78377751
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10248125	0.80[CEU][hapmap]
rs10248911	1.00[ASN][1000 genomes]
rs10953684	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1207862	0.95[CEU][hapmap]
rs1207868	0.96[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap]
rs1207870	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1207871	0.95[CEU][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1207872	0.95[CEU][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1207874	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1207875	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1207882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1207895	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.96[ASN][1000 genomes]
rs1207896	0.96[CEU][hapmap];0.82[GIH][hapmap];0.90[TSI][hapmap]
rs1207898	0.95[CEU][hapmap]
rs1207901	0.96[CEU][hapmap]
rs1209401	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1859327	0.82[CHB][hapmap]
rs2210115	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.97[ASN][1000 genomes]
rs2774058	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs67890238	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6951046	0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6965150	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7790151	0.96[CEU][hapmap]
rs944279	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1019355	chr7:78319575-78399845	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv607657	chr7:78329795-78483211	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1207881	SEMA3C	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78363600-78380400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:78372400-78391600	Weak transcription	Pancreas	Pancrea
3	chr7:78372400-78395200	Weak transcription	Aorta	Aorta
4	chr7:78373800-78378400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:78374200-78379200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr7:78374200-78379200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr7:78374800-78379800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr7:78375000-78379000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr7:78375400-78378400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr7:78375800-78381000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:78376000-78378400	Weak transcription	Brain Hippocampus Middle	brain
12	chr7:78376000-78378400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr7:78376000-78380600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr7:78376000-78384600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr7:78376200-78378200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr7:78377200-78378200	Weak transcription	Fetal Brain Male	brain
17	chr7:78377200-78378600	Weak transcription	Fetal Brain Female	brain
18	chr7:78377200-78381000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr7:78377200-78384000	Weak transcription	Psoas Muscle	Psoas
20	chr7:78377200-78385400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr7:78377400-78377800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr7:78377400-78378400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr7:78377400-78378600	Weak transcription	Brain Substantia Nigra	brain
24	chr7:78377400-78380600	Weak transcription	Brain Anterior Caudate	brain
25	chr7:78377600-78378000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr7:78377600-78378000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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