Variant report

Variant	rs6439638
Chromosome Location	chr3:136057832-136057833
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136050884..136053004-chr3:136057100..136060594,3	K562	blood:
2	chr3:136056870..136058632-chr3:136058786..136060783,2	K562	blood:
3	chr3:136056019..136058370-chr3:136058786..136061509,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10513002	1.00[CHB][hapmap]
rs10935178	1.00[CHB][hapmap]
rs12330258	0.84[AFR][1000 genomes]
rs1279425	0.85[YRI][hapmap]
rs16843879	1.00[CHB][hapmap]
rs16843978	1.00[CHB][hapmap]
rs16843991	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs17199978	1.00[CHB][hapmap]
rs17266364	1.00[CHB][hapmap]
rs28396702	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28812220	0.92[EUR][1000 genomes]
rs34165586	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34523567	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35058853	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375192	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35644083	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs3755636	0.85[YRI][hapmap]
rs3872588	1.00[CHB][hapmap]
rs4678428	0.85[YRI][hapmap]
rs5026242	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs548288	0.85[YRI][hapmap]
rs55797013	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56251259	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576771	0.85[YRI][hapmap]
rs6439642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs67214626	0.93[EUR][1000 genomes]
rs6766450	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6773495	1.00[CHB][hapmap]
rs6773604	1.00[CHB][hapmap]
rs6776841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785225	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6800570	1.00[CHB][hapmap]
rs6804194	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620314	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs7622833	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7650075	1.00[CHB][hapmap]
rs9809184	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811261	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9811490	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812319	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs9812513	1.00[CEU][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9819496	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826146	1.00[CEU][hapmap];0.85[YRI][hapmap];0.92[EUR][1000 genomes]
rs9831321	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9833162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843348	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9843801	1.00[CEU][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9850383	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9853387	0.84[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9854328	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9860801	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9868120	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9872326	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv4025	chr3:136017458-136065622	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6439638	SCN9A	trans	cerebellum	SCAN
rs6439638	RNF184	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135999800-136061200	Weak transcription	Hela-S3	cervix
2	chr3:136039000-136072400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:136039200-136062400	Weak transcription	Fetal Heart	heart
4	chr3:136040400-136062800	Weak transcription	Stomach Mucosa	stomach
5	chr3:136040600-136061400	Weak transcription	Small Intestine	intestine
6	chr3:136042400-136058200	Weak transcription	Psoas Muscle	Psoas
7	chr3:136042400-136078800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:136042600-136072600	Strong transcription	Dnd41	blood
9	chr3:136043400-136098600	Weak transcription	Fetal Brain Male	brain
10	chr3:136043600-136082000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:136043800-136070400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:136045200-136060800	Strong transcription	Liver	Liver
13	chr3:136045200-136062000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:136045600-136079200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:136046200-136060000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:136047600-136098000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:136047800-136068200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:136047800-136074800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr3:136048200-136060200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:136048400-136062800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:136048800-136062600	Weak transcription	NHEK	skin
22	chr3:136049000-136062800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:136050800-136062800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:136051000-136062200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:136051000-136062400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:136051000-136062800	Strong transcription	Adipose Nuclei	Adipose
27	chr3:136051000-136063600	Strong transcription	Fetal Thymus	thymus
28	chr3:136051000-136069800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:136051200-136063600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:136051600-136063600	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr3:136051600-136063600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:136051600-136064800	Strong transcription	Primary T cells from cord blood	blood
33	chr3:136051600-136069200	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr3:136051600-136070800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr3:136051800-136060400	Strong transcription	Fetal Brain Female	brain
36	chr3:136051800-136062400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr3:136052000-136059600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr3:136052000-136061400	Strong transcription	Fetal Intestine Large	intestine
39	chr3:136052000-136062400	Strong transcription	Placenta	Placenta
40	chr3:136052000-136062600	Strong transcription	Left Ventricle	heart
41	chr3:136052000-136063200	Strong transcription	Primary B cells from cord blood	blood
42	chr3:136052000-136063400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:136052000-136063600	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr3:136052200-136063400	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:136052200-136063400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr3:136052200-136069200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:136052400-136060600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:136052800-136070800	Strong transcription	Primary B cells from peripheral blood	blood
49	chr3:136053000-136059800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:136053000-136060600	Strong transcription	Rectal Mucosa Donor 29	rectum

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