Variant report

Variant	rs3796129
Chromosome Location	chr3:196199204-196199205
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:196198167-196199642	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:196192779..196196308-chr3:196197005..196200589,3	K562	blood:
2	chr3:196192358..196194279-chr3:196199089..196201491,2	K562	blood:
3	chr3:196013817..196016385-chr3:196199052..196201409,2	MCF-7	breast:
4	chr3:196194808..196197230-chr3:196197915..196199968,2	K562	blood:
5	chr3:196197868..196200797-chr3:196203999..196206906,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000273013	TF binding region
ENSG00000161217	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11185543	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11707744	0.89[ASN][1000 genomes]
rs11718980	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11719920	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12632592	0.89[ASN][1000 genomes]
rs12635457	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13084212	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13098146	0.96[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34196595	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34722299	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4393941	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916431	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916497	0.81[CHB][hapmap];0.90[ASN][1000 genomes]
rs4916498	0.93[ASN][1000 genomes]
rs4916499	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5016648	0.91[ASN][1000 genomes]
rs55997345	0.87[ASN][1000 genomes]
rs6772271	0.85[ASN][1000 genomes]
rs6775484	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6803161	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71630192	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7433483	0.89[ASN][1000 genomes]
rs7611980	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7612450	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7629990	0.82[YRI][hapmap]
rs7643192	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7646174	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7646273	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7647487	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837568	0.96[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9844068	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9864836	0.81[CHB][hapmap];0.96[CHD][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs9869437	0.81[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9872866	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv469831	chr3:196071603-196235225	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv482542	chr3:196071603-196235225	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
10	nsv878185	chr3:196158773-196199204	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv878186	chr3:196158773-196219794	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3796129	TCTEX1D2	cis	parietal	SCAN
rs3796129	RNF168	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196182200-196213600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:196191800-196216800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:196193400-196200200	Weak transcription	Fetal Kidney	kidney
4	chr3:196193400-196209400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:196193600-196214600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr3:196194200-196202200	Strong transcription	HUVEC	blood vessel
7	chr3:196194200-196215000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:196194200-196217400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr3:196194400-196211200	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:196194400-196216600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:196194600-196214600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:196194600-196214800	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:196194600-196215800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:196194800-196215000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:196195000-196214800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:196195200-196202400	Strong transcription	Hela-S3	cervix
17	chr3:196195200-196215200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:196195400-196214800	Strong transcription	Liver	Liver
19	chr3:196195400-196215600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr3:196195600-196202400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:196195600-196214400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:196195600-196215000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:196195800-196214800	Strong transcription	Dnd41	blood
24	chr3:196196000-196205400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:196196200-196201600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr3:196196600-196202400	Strong transcription	K562	blood
27	chr3:196196800-196199400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:196196800-196200200	Weak transcription	Fetal Brain Male	brain
29	chr3:196196800-196202200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr3:196196800-196207200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:196196800-196208000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:196196800-196214600	Strong transcription	Fetal Stomach	stomach
33	chr3:196196800-196214800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:196196800-196217000	Strong transcription	Fetal Intestine Small	intestine
35	chr3:196197000-196216800	Strong transcription	GM12878-XiMat	blood
36	chr3:196197000-196220000	Weak transcription	Stomach Mucosa	stomach
37	chr3:196197200-196214800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr3:196197200-196223800	Strong transcription	Fetal Thymus	thymus
39	chr3:196197400-196201200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:196197400-196201200	Strong transcription	Colonic Mucosa	Colon
41	chr3:196197400-196201800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:196197400-196202200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:196197400-196202200	Strong transcription	Rectal Smooth Muscle	rectum
44	chr3:196197400-196202200	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr3:196197400-196202200	Strong transcription	Osteobl	bone
46	chr3:196197400-196202400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:196197400-196202400	Strong transcription	Primary T cells from cord blood	blood
48	chr3:196197400-196202400	Strong transcription	Brain Substantia Nigra	brain
49	chr3:196197400-196202600	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr3:196197400-196202600	Strong transcription	Adipose Nuclei	Adipose

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