Variant report

Variant	rs9864836
Chromosome Location	chr3:196200737-196200738
allele	C/T
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	POLR2A	chr3:196200666-196201163	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:196200641-196201096	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:196200665-196201152	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:196200717-196200752	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:196192358..196194279-chr3:196199089..196201491,2	K562	blood:
2	chr3:196013817..196016385-chr3:196199052..196201409,2	MCF-7	breast:
3	chr3:196197868..196200797-chr3:196203999..196206906,2	K562	blood:

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

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11185543	0.89[ASN][1000 genomes]
rs11707744	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11718980	0.89[ASN][1000 genomes]
rs11719920	0.91[ASN][1000 genomes]
rs12632592	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12635457	0.95[ASN][1000 genomes]
rs13084212	0.89[ASN][1000 genomes]
rs13094241	0.81[EUR][1000 genomes]
rs13098146	0.92[CHD][hapmap];0.91[ASN][1000 genomes]
rs13099664	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34196595	0.92[ASN][1000 genomes]
rs3796129	0.81[CHB][hapmap];0.96[CHD][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs4244200	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4393941	0.91[ASN][1000 genomes]
rs4916431	0.91[ASN][1000 genomes]
rs4916497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916498	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4916499	0.91[ASN][1000 genomes]
rs5016648	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55997345	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6772271	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6775484	0.91[ASN][1000 genomes]
rs6803161	0.95[ASN][1000 genomes]
rs71630192	0.89[ASN][1000 genomes]
rs7430950	1.00[ASW][hapmap]
rs7433483	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7611980	0.89[ASN][1000 genomes]
rs7612450	0.89[ASN][1000 genomes]
rs7643192	0.89[ASN][1000 genomes]
rs7646174	0.89[ASN][1000 genomes]
rs7646273	0.89[ASN][1000 genomes]
rs7647487	0.91[ASN][1000 genomes]
rs7648887	0.82[CEU][hapmap]
rs9837568	0.84[MEX][hapmap]
rs9843876	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9856006	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9869437	0.84[MEX][hapmap]
rs9872866	0.94[ASN][1000 genomes]

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	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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9864836	RNF168	cis	cerebellum	SCAN
rs9864836	FBXO45	Cis_1M	lymphoblastoid	RTeQTL
rs9864836	MGC33212	cis	multi-tissue	Pritchard
rs9864836	TCTEX1D2	cis	parietal	SCAN
rs9864836	UBXD7	Cis_1M	lymphoblastoid	RTeQTL

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	chr3:196193400-196209400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr3:196193600-196214600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:196194200-196202200	Strong transcription	HUVEC	blood vessel
6	chr3:196194200-196215000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:196194200-196217400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr3:196194400-196211200	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:196194400-196216600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:196194600-196214600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:196194600-196214800	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:196194600-196215800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:196194800-196215000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:196195000-196214800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:196195200-196202400	Strong transcription	Hela-S3	cervix
16	chr3:196195200-196215200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:196195400-196214800	Strong transcription	Liver	Liver
18	chr3:196195400-196215600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr3:196195600-196202400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:196195600-196214400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:196195600-196215000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:196195800-196214800	Strong transcription	Dnd41	blood
23	chr3:196196000-196205400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:196196200-196201600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr3:196196600-196202400	Strong transcription	K562	blood
26	chr3:196196800-196202200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr3:196196800-196207200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:196196800-196208000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:196196800-196214600	Strong transcription	Fetal Stomach	stomach
30	chr3:196196800-196214800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:196196800-196217000	Strong transcription	Fetal Intestine Small	intestine
32	chr3:196197000-196216800	Strong transcription	GM12878-XiMat	blood
33	chr3:196197000-196220000	Weak transcription	Stomach Mucosa	stomach
34	chr3:196197200-196214800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr3:196197200-196223800	Strong transcription	Fetal Thymus	thymus
36	chr3:196197400-196201200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:196197400-196201200	Strong transcription	Colonic Mucosa	Colon
38	chr3:196197400-196201800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:196197400-196202200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:196197400-196202200	Strong transcription	Rectal Smooth Muscle	rectum
41	chr3:196197400-196202200	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:196197400-196202200	Strong transcription	Osteobl	bone
43	chr3:196197400-196202400	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:196197400-196202400	Strong transcription	Primary T cells from cord blood	blood
45	chr3:196197400-196202400	Strong transcription	Brain Substantia Nigra	brain
46	chr3:196197400-196202600	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:196197400-196202600	Strong transcription	Adipose Nuclei	Adipose
48	chr3:196197400-196214600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:196197400-196214600	Strong transcription	Thymus	Thymus
50	chr3:196197600-196202200	Strong transcription	Brain Anterior Caudate	brain

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