Variant report

Variant	rs1229678
Chromosome Location	chr7:26460409-26460410
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:26436548..26440946-chr7:26456240..26460952,5	K562	blood:
2	chr7:26456740..26460595-chr7:26476772..26480334,4	K562	blood:
3	chr7:26451757..26454537-chr7:26460111..26461633,2	K562	blood:
4	chr7:26448654..26450705-chr7:26456619..26460704,3	K562	blood:
5	chr7:26459230..26461137-chr7:26676682..26679366,2	K562	blood:

Variant related genes	Relation type
ENSG00000214870	Chromatin interaction
ENSG00000222004	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10951138	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1229673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1229677	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1229679	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1229681	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1229684	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1236948	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1919936	0.87[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1997358	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1997359	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2698729	0.81[ASN][1000 genomes]
rs34041259	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9791381	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv606461	chr7:26460409-26485860	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1229678	C7orf46	cis	cerebellum	SCAN
rs1229678	STK31	cis	parietal	SCAN
rs1229678	C7orf41	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26446000-26471200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr7:26453400-26468400	Weak transcription	Pancreas	Pancrea
3	chr7:26453600-26462600	Weak transcription	Lung	lung
4	chr7:26458000-26465400	Weak transcription	Fetal Lung	lung
5	chr7:26458200-26463400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:26458400-26461400	Enhancers	K562	blood
7	chr7:26459400-26461400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr7:26459800-26460600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:26459800-26460800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:26459800-26460800	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr7:26459800-26460800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr7:26459800-26461400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr7:26460000-26460800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:26460000-26460800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:26460200-26460600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:26460200-26460800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:26460200-26460800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr7:26460200-26460800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr7:26460200-26461000	Enhancers	Primary hematopoietic stem cells	blood
20	chr7:26460200-26461200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr7:26460200-26461400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:26460400-26460600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr7:26460400-26460800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:26460400-26460800	Enhancers	H9 Cell Line	embryonic stem cell
25	chr7:26460400-26460800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr7:26460400-26460800	Enhancers	Fetal Kidney	kidney
27	chr7:26460400-26461200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr7:26460400-26461400	Enhancers	H1 Cell Line	embryonic stem cell
29	chr7:26460400-26461600	Enhancers	HUES64 Cell Line	embryonic stem cell

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