Variant report

Variant	rs35375192
Chromosome Location	chr3:136175525-136175526
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10513002	1.00[CHB][hapmap]
rs10513016	1.00[CHB][hapmap]
rs12330800	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12695649	0.81[GIH][hapmap]
rs13321721	0.81[GIH][hapmap]
rs13433980	0.95[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap]
rs1484250	0.95[CEU][hapmap];0.85[YRI][hapmap]
rs16843879	1.00[CHB][hapmap]
rs16843978	1.00[CHB][hapmap]
rs16843991	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17199978	1.00[CHB][hapmap]
rs17266364	1.00[CHB][hapmap]
rs17364492	0.81[GIH][hapmap]
rs17365351	1.00[CHB][hapmap]
rs28396702	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28634226	0.81[GIH][hapmap]
rs28889583	0.82[EUR][1000 genomes]
rs34165586	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34523567	0.84[EUR][1000 genomes]
rs34757183	0.81[GIH][hapmap]
rs34804893	0.83[GIH][hapmap]
rs34913797	0.81[GIH][hapmap]
rs34962604	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35058853	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35644083	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3931416	1.00[CHB][hapmap];0.89[YRI][hapmap]
rs3932048	0.95[CEU][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes]
rs5026242	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55797013	0.80[EUR][1000 genomes]
rs56040643	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56251259	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6439638	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]
rs6439642	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766450	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6768743	0.81[GIH][hapmap]
rs6769934	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773495	1.00[CHB][hapmap]
rs6773604	1.00[CHB][hapmap]
rs6776841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6782151	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs6783337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6789761	0.84[EUR][1000 genomes]
rs6799368	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804194	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6806123	0.81[GIH][hapmap]
rs699165	0.89[YRI][hapmap]
rs7612160	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7615706	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7620314	0.81[CEU][hapmap];0.87[MEX][hapmap];0.85[YRI][hapmap]
rs7621017	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7622833	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7644346	0.95[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap]
rs7644471	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs7646563	1.00[CHB][hapmap]
rs7646723	1.00[CHB][hapmap]
rs7648591	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7650075	1.00[CHB][hapmap]
rs9809184	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9811261	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9811490	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9812319	1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9812513	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9812579	0.81[GIH][hapmap]
rs9813691	0.81[GIH][hapmap]
rs9819496	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9820513	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap]
rs9826146	1.00[CEU][hapmap]
rs9831321	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9833162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9837158	0.81[GIH][hapmap]
rs9843801	1.00[CEU][hapmap]
rs9845950	0.95[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap]
rs9850383	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9853387	0.84[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9854084	0.89[YRI][hapmap]
rs9857966	0.81[GIH][hapmap]
rs9858457	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860801	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9866535	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868120	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9880211	0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv877522	chr3:136088038-136241028	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv877524	chr3:136112109-136295283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active 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
rs35375192	ZBTB38	cis	cerebellum	SCAN
rs35375192	SCN9A	trans	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136139800-136175800	Weak transcription	Right Ventricle	heart
2	chr3:136140000-136175800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:136161000-136176000	Weak transcription	NHLF	lung
4	chr3:136161800-136176000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:136170600-136175800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:136172400-136178600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:136172600-136177400	ZNF genes & repeats	Fetal Muscle Leg	muscle
8	chr3:136172800-136177200	Strong transcription	Placenta Amnion	Placenta Amnion
9	chr3:136173000-136177000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:136173000-136177200	ZNF genes & repeats	Adipose Nuclei	Adipose
11	chr3:136173000-136178200	ZNF genes & repeats	Fetal Intestine Small	intestine
12	chr3:136173000-136181400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:136173200-136176800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:136173200-136176800	ZNF genes & repeats	Brain Germinal Matrix	brain
15	chr3:136173200-136177600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:136173200-136177600	ZNF genes & repeats	Fetal Intestine Large	intestine
17	chr3:136173200-136178400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
18	chr3:136173400-136175800	Strong transcription	Fetal Thymus	thymus
19	chr3:136173400-136176600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
20	chr3:136173400-136177200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:136173400-136177800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
22	chr3:136173400-136178000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
23	chr3:136173600-136176400	ZNF genes & repeats	Fetal Kidney	kidney
24	chr3:136173600-136177400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
25	chr3:136173600-136177600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:136173600-136178000	ZNF genes & repeats	Primary B cells from cord blood	blood
27	chr3:136173800-136176800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
28	chr3:136173800-136176800	ZNF genes & repeats	Fetal Brain Female	brain
29	chr3:136173800-136177000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
30	chr3:136173800-136177800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:136174000-136176400	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
32	chr3:136174000-136176600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
33	chr3:136174000-136176800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
34	chr3:136174000-136177000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
35	chr3:136174000-136177200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:136174000-136177600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:136174000-136177800	ZNF genes & repeats	Fetal Lung	lung
38	chr3:136174000-136178000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:136174000-136178000	ZNF genes & repeats	GM12878-XiMat	blood
40	chr3:136174000-136178400	ZNF genes & repeats	Primary T cells from cord blood	blood
41	chr3:136174000-136178600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
42	chr3:136174200-136176400	ZNF genes & repeats	Osteobl	bone
43	chr3:136174200-136176600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:136174200-136176600	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
45	chr3:136174200-136176600	ZNF genes & repeats	Colon Smooth Muscle	Colon
46	chr3:136174200-136176800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:136174200-136176800	ZNF genes & repeats	Brain Anterior Caudate	brain
48	chr3:136174200-136176800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
49	chr3:136174200-136176800	ZNF genes & repeats	Ovary	ovary
50	chr3:136174200-136177000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood

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