Variant report

Variant	rs3768329
Chromosome Location	chr1:228278108-228278109
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228274276-228290284	K562	blood:	n/a	n/a
2	POLR2A	chr1:228274933-228281306	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:228276335-228278744	K562	blood:	n/a	n/a
4	POLR2A	chr1:228277305-228278601	GM12891	blood:	n/a	n/a
5	POLR2A	chr1:228277692-228278271	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:228276358-228278146	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:228276225-228279615	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:228277290-228278661	HL-60	blood:	n/a	n/a
9	MXI1	chr1:228278039-228278847	IMR90	lung:	n/a	n/a
10	POLR2A	chr1:228277242-228278533	K562	blood:	n/a	n/a
11	HEY1	chr1:228277434-228278784	K562	blood:	n/a	n/a
12	POLR2A	chr1:228274170-228289426	HepG2	liver:	n/a	n/a
13	POLR2A	chr1:228277256-228278117	GM12892	blood:	n/a	n/a
14	POLR2A	chr1:228276366-228280674	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:228276326-228278305	K562	blood:	n/a	n/a
16	POLR2A	chr1:228277397-228278280	GM12891	blood:	n/a	n/a
17	POLR2A	chr1:228276275-228279657	K562	blood:	n/a	n/a
18	POLR2A	chr1:228277402-228278747	GM19193	blood:	n/a	n/a
19	POLR2A	chr1:228277314-228278803	K562	blood:	n/a	n/a
20	POLR2A	chr1:228275014-228282866	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:228276361-228281309	A549	lung:	n/a	n/a
22	POLR2A	chr1:228277357-228278347	GM12892	blood:	n/a	n/a
23	POLR2A	chr1:228274271-228281353	HepG2	liver:	n/a	n/a
24	POLR2A	chr1:228277315-228278155	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr1:228277394-228278140	SK-N-MC	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228274118..228278669-chr1:228294195..228297645,6	MCF-7	breast:

No data

Variant related genes	Relation type
ARF1	TF binding region
ENSG00000162910	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1034792	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs1048503	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10495278	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs10916262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577983	0.80[ASN][1000 genomes]
rs11578623	0.80[ASN][1000 genomes]
rs11582265	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582704	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584499	0.85[TSI][hapmap]
rs11589007	0.80[ASN][1000 genomes]
rs11589040	1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs11589467	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.80[ASN][1000 genomes]
rs11589513	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590118	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs1188975	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1188977	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs12033088	0.82[EUR][1000 genomes]
rs12048010	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1620734	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1745422	0.82[EUR][1000 genomes]
rs17621519	0.80[ASN][1000 genomes]
rs1909647	0.80[ASN][1000 genomes]
rs2070960	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2295995	0.89[EUR][1000 genomes]
rs3738680	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3738681	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3768330	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820624	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41270175	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs41270177	0.82[EUR][1000 genomes]
rs4363416	0.84[ASN][1000 genomes]
rs4546914	0.80[ASN][1000 genomes]
rs4653894	1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs4653897	0.82[EUR][1000 genomes]
rs56888086	0.82[ASN][1000 genomes]
rs57146523	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57657087	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60213528	0.84[ASN][1000 genomes]
rs61825130	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61825131	0.82[EUR][1000 genomes]
rs61825135	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs708126	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs72756204	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72756209	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7530812	0.82[ASN][1000 genomes]
rs7539664	0.85[TSI][hapmap]
rs822727	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs860301	0.98[EUR][1000 genomes]
rs882451	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[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	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3768329	OBSCN	cis	cerebellum	SCAN
rs3768329	MIXL1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228271600-228278600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr1:228272400-228279400	Genic enhancers	Fetal Muscle Leg	muscle
3	chr1:228272400-228280000	Genic enhancers	Fetal Thymus	thymus
4	chr1:228272400-228284400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:228272600-228278400	Enhancers	Small Intestine	intestine
6	chr1:228272600-228280200	Enhancers	Fetal Heart	heart
7	chr1:228272800-228278600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:228272800-228278600	Genic enhancers	Fetal Stomach	stomach
9	chr1:228273000-228279200	Genic enhancers	Fetal Intestine Small	intestine
10	chr1:228273000-228284200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:228273400-228278200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:228273400-228279000	Genic enhancers	HepG2	liver
13	chr1:228273400-228280200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr1:228273400-228285200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:228273600-228278200	Weak transcription	Fetal Brain Male	brain
16	chr1:228273600-228278200	Genic enhancers	K562	blood
17	chr1:228273600-228281800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:228273800-228279200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:228274000-228279200	Enhancers	Colon Smooth Muscle	Colon
20	chr1:228274000-228280600	Enhancers	Psoas Muscle	Psoas
21	chr1:228274200-228281200	Genic enhancers	Liver	Liver
22	chr1:228274600-228278200	Genic enhancers	A549	lung
23	chr1:228274600-228278800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:228274600-228278800	Enhancers	Placenta Amnion	Placenta Amnion
25	chr1:228274600-228280600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:228274800-228278800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
27	chr1:228274800-228279200	Genic enhancers	Fetal Intestine Large	intestine
28	chr1:228275200-228280800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:228275200-228282000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:228275400-228278200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:228275400-228279200	Genic enhancers	Fetal Muscle Trunk	muscle
32	chr1:228275400-228281200	Genic enhancers	Gastric	stomach
33	chr1:228275400-228281400	Genic enhancers	Primary B cells from peripheral blood	blood
34	chr1:228275600-228278200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
35	chr1:228275600-228279200	Genic enhancers	Thymus	Thymus
36	chr1:228275600-228279400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
37	chr1:228275600-228280200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:228275600-228281200	Genic enhancers	Primary T cells fromperipheralblood	blood
39	chr1:228275800-228278800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:228275800-228279400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:228275800-228279400	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
42	chr1:228275800-228279800	Enhancers	Primary hematopoietic stem cells	blood
43	chr1:228275800-228280000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:228275800-228280200	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:228275800-228281000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:228275800-228286600	Weak transcription	Fetal Kidney	kidney
47	chr1:228276000-228278400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:228276000-228279000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:228276000-228280400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr1:228276000-228281000	Genic enhancers	Primary T helper cells fromperipheralblood	blood

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