Variant report

Variant	rs7858435
Chromosome Location	chr9:94651415-94651416
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:94651409-94651776	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr9:94651397-94651805	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr9:94651407-94651816	K562	blood:	n/a	n/a
4	CTCF	chr9:94651397-94651862	K562	blood:	n/a	n/a
5	CTCF	chr9:94651355-94651808	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:94650894..94652826-chr9:94665751..94669153,3	K562	blood:
2	chr9:94650853..94651554-chr9:94712434..94713072,2	MCF-7	breast:
3	chr9:94641817..94643317-chr9:94650910..94653000,2	K562	blood:

Variant related genes	Relation type
ROR2	TF binding region
ENSG00000169071	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10116351	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10116962	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761132	0.82[ASN][1000 genomes]
rs10761135	0.87[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10820910	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs10992154	0.83[CEU][hapmap];0.87[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11795130	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12685595	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1528363	0.83[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs1528364	0.83[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs1534533	0.83[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1881391	0.95[JPT][hapmap]
rs4744111	0.83[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs4744112	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4744114	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62565675	0.83[ASN][1000 genomes]
rs6479377	0.82[ASN][1000 genomes]
rs6479387	0.95[JPT][hapmap]
rs7047587	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7870049	0.83[CHB][hapmap];0.82[JPT][hapmap];0.81[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	nsv1045332	chr9:94352661-94656016	Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv530946	chr9:94633154-94715023	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7858435	SPTLC1	cis	multi-tissue	Pritchard

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94646000-94651600	Enhancers	K562	blood
2	chr9:94646000-94652600	Enhancers	Ovary	ovary
3	chr9:94646000-94654800	Enhancers	Fetal Lung	lung
4	chr9:94646600-94654600	Enhancers	Fetal Stomach	stomach
5	chr9:94646600-94658200	Weak transcription	Fetal Heart	heart
6	chr9:94647200-94652600	Enhancers	Fetal Intestine Large	intestine
7	chr9:94647800-94652200	Weak transcription	Brain Substantia Nigra	brain
8	chr9:94648800-94653200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:94648800-94658400	Weak transcription	Pancreas	Pancrea
10	chr9:94648800-94661000	Weak transcription	Spleen	Spleen
11	chr9:94649000-94651600	Enhancers	Fetal Intestine Small	intestine
12	chr9:94649400-94663200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr9:94649800-94658400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:94650000-94653400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:94650000-94662400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:94650400-94653600	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr9:94650600-94651600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:94650600-94652200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr9:94650600-94654600	Enhancers	Rectal Smooth Muscle	rectum
20	chr9:94650800-94651600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
21	chr9:94650800-94651600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
22	chr9:94650800-94651600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
23	chr9:94650800-94651800	Enhancers	Esophagus	oesophagus
24	chr9:94650800-94652000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:94650800-94652000	Enhancers	Colonic Mucosa	Colon
26	chr9:94650800-94652000	Enhancers	Lung	lung
27	chr9:94650800-94652000	Enhancers	Right Atrium	heart
28	chr9:94650800-94652600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr9:94651000-94651800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:94651000-94652200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:94651000-94652400	Bivalent Enhancer	Placenta	Placenta
32	chr9:94651000-94652800	Weak transcription	Fetal Kidney	kidney
33	chr9:94651200-94653200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:94651200-94659200	Enhancers	Colon Smooth Muscle	Colon
35	chr9:94651200-94665000	Weak transcription	NHLF	lung
36	chr9:94651400-94651600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:94651400-94651600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr9:94651400-94651800	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr9:94651400-94651800	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr9:94651400-94652400	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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