Variant report

Variant	rs6799699
Chromosome Location	chr3:136458866-136458867
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136457793..136459867-chr3:136469350..136471388,2	MCF-7	breast:
2	chr3:136457290..136459900-chr3:136462438..136464263,2	K562	blood:

Variant related genes	Relation type
ENSG00000118007	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10155016	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10155017	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10513014	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs12107125	0.92[AFR][1000 genomes]
rs12635723	0.85[LWK][hapmap];0.92[YRI][hapmap]
rs13433980	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1484250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1872240	0.98[EUR][1000 genomes]
rs28682370	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34992220	0.86[CEU][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap]
rs3932048	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap]
rs4336059	0.83[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap]
rs4678438	0.81[LWK][hapmap];0.92[YRI][hapmap]
rs59931907	0.81[AFR][1000 genomes]
rs6439655	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs6763239	0.81[EUR][1000 genomes]
rs6765239	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs6771713	1.00[ASW][hapmap];1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772759	0.81[EUR][1000 genomes]
rs6782151	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs6789329	0.91[CEU][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6800969	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs73230077	0.81[ASN][1000 genomes]
rs73230078	0.81[ASN][1000 genomes]
rs7612160	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap]
rs7623824	0.94[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap]
rs7626418	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7629905	0.81[EUR][1000 genomes]
rs7644346	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7644471	0.89[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap]
rs9813596	0.82[AFR][1000 genomes]
rs9818372	0.81[EUR][1000 genomes]
rs9820513	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs9828068	0.81[EUR][1000 genomes]
rs9839574	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap]
rs9845762	0.85[LWK][hapmap];0.92[YRI][hapmap]
rs9845950	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9853960	0.83[EUR][1000 genomes]
rs9869361	0.81[EUR][1000 genomes]
rs9869957	1.00[CEU][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9881078	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6799699	SCN9A	trans	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136432400-136468200	Weak transcription	Aorta	Aorta
2	chr3:136433200-136462600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:136438800-136461200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:136445400-136460000	Weak transcription	Gastric	stomach
5	chr3:136446400-136460000	Weak transcription	K562	blood
6	chr3:136448000-136460800	Weak transcription	Brain Germinal Matrix	brain
7	chr3:136448200-136459800	Weak transcription	Osteobl	bone
8	chr3:136448200-136460000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:136448200-136467600	Weak transcription	HSMM	muscle
10	chr3:136448200-136467800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:136448200-136467800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:136448200-136467800	Weak transcription	HSMMtube	muscle
13	chr3:136448400-136459800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:136448600-136460200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:136448600-136462800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:136448600-136463800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:136448600-136467600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:136449000-136470000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:136449800-136462400	Weak transcription	Dnd41	blood
20	chr3:136450200-136461200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:136450400-136460000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:136450400-136467800	Weak transcription	Psoas Muscle	Psoas
23	chr3:136450600-136467800	Weak transcription	Primary B cells from cord blood	blood
24	chr3:136450800-136462800	Weak transcription	Thymus	Thymus
25	chr3:136450800-136467800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:136450800-136467800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:136450800-136467800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr3:136450800-136469000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:136451000-136467800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:136451400-136459600	Weak transcription	NHEK	skin
31	chr3:136453200-136466000	Weak transcription	Placenta	Placenta
32	chr3:136453600-136467800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:136453800-136459600	Weak transcription	A549	lung
34	chr3:136453800-136464000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:136453800-136467600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:136454000-136459200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:136454200-136462000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:136454200-136462400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:136454200-136462800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:136454200-136464200	Weak transcription	Right Atrium	heart
41	chr3:136454200-136464200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:136454200-136465400	Weak transcription	Adipose Nuclei	Adipose
43	chr3:136454200-136465400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:136454200-136467800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:136454200-136469200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr3:136454200-136470000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:136454400-136459600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:136454400-136459800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr3:136454400-136461800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:136454400-136464200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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