Variant report

Variant	rs1188975
Chromosome Location	chr1:228277690-228277691
allele	A/G
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	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	SPI1	chr1:228277157-228277711	HL-60	blood:	n/a	chr1:228277441-228277454 chr1:228277442-228277451
6	RCOR1	chr1:228277208-228277718	GM12878	blood:	n/a	n/a
7	SPI1	chr1:228277209-228277695	GM12878	blood:	n/a	chr1:228277441-228277454 chr1:228277442-228277451
8	MXI1	chr1:228277586-228277706	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:228277472-228277955	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:228276358-228278146	GM12892	blood:	n/a	n/a
11	POLR2A	chr1:228276225-228279615	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:228277290-228278661	HL-60	blood:	n/a	n/a
13	POLR2A	chr1:228277613-228277905	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr1:228277242-228278533	K562	blood:	n/a	n/a
15	HEY1	chr1:228277434-228278784	K562	blood:	n/a	n/a
16	POLR2A	chr1:228274170-228289426	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:228276993-228278002	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr1:228277576-228278068	HCT-116	colon:	n/a	n/a
19	POLR2A	chr1:228277256-228278117	GM12892	blood:	n/a	n/a
20	POLR2A	chr1:228276366-228280674	GM12878	blood:	n/a	n/a
21	MYC	chr1:228277672-228277729	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr1:228276326-228278305	K562	blood:	n/a	n/a
23	POLR2A	chr1:228277426-228277958	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:228276334-228277960	GM12891	blood:	n/a	n/a
25	POLR2A	chr1:228277397-228278280	GM12891	blood:	n/a	n/a
26	POLR2A	chr1:228277489-228277810	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr1:228276275-228279657	K562	blood:	n/a	n/a
28	HEY1	chr1:228277505-228277949	K562	blood:	n/a	n/a
29	TBL1XR1	chr1:228277338-228277718	GM12878	blood:	n/a	n/a
30	NFATC1	chr1:228277181-228277743	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:228277560-228277842	Hela-S3	cervix:	n/a	n/a
32	WRNIP1	chr1:228276397-228277961	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:228277402-228278747	GM19193	blood:	n/a	n/a
34	POLR2A	chr1:228277314-228278803	K562	blood:	n/a	n/a
35	SPI1	chr1:228276973-228277899	GM12878	blood:	n/a	chr1:228277441-228277454 chr1:228277442-228277451
36	POLR2A	chr1:228275014-228282866	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:228276361-228281309	A549	lung:	n/a	n/a
38	POLR2A	chr1:228277552-228277996	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr1:228277357-228278347	GM12892	blood:	n/a	n/a
40	POLR2A	chr1:228274271-228281353	HepG2	liver:	n/a	n/a
41	POLR2A	chr1:228277658-228277837	A549	lung:	n/a	n/a
42	POLR2A	chr1:228277583-228277757	HepG2	liver:	n/a	n/a
43	POLR2A	chr1:228277315-228278155	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr1:228277394-228278140	SK-N-MC	brain:	n/a	n/a
45	POLR2A	chr1:228277678-228277926	GM12891	blood:	n/a	n/a
46	SPI1	chr1:228277110-228277840	HL-60	blood:	n/a	chr1:228277441-228277454 chr1:228277442-228277451
47	POLR2A	chr1:228277558-228277957	HepG2	liver:	n/a	n/a

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

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

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1034792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1048503	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes]
rs10916261	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1094602	0.82[ASN][1000 genomes]
rs11582265	0.91[EUR][1000 genomes]
rs11582704	0.91[EUR][1000 genomes]
rs11584499	0.86[JPT][hapmap]
rs1188977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13374948	0.84[CHB][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1620734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1745420	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2070960	0.93[EUR][1000 genomes]
rs2107905	0.86[ASN][1000 genomes]
rs2295995	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3738680	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes]
rs3738681	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes]
rs3768329	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3768330	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3820624	0.91[EUR][1000 genomes]
rs41270177	0.99[ASN][1000 genomes]
rs4653533	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4653897	0.97[ASN][1000 genomes]
rs4653906	0.93[CHB][hapmap]
rs61825135	0.84[EUR][1000 genomes]
rs6668719	0.85[CHB][hapmap]
rs708126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537552	0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs7539664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs822727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860301	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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

No data

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	chr1:228273600-228277800	Genic enhancers	Dnd41	blood
16	chr1:228273600-228278200	Weak transcription	Fetal Brain Male	brain
17	chr1:228273600-228278200	Genic enhancers	K562	blood
18	chr1:228273600-228281800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:228273800-228279200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:228274000-228279200	Enhancers	Colon Smooth Muscle	Colon
21	chr1:228274000-228280600	Enhancers	Psoas Muscle	Psoas
22	chr1:228274200-228281200	Genic enhancers	Liver	Liver
23	chr1:228274600-228278200	Genic enhancers	A549	lung
24	chr1:228274600-228278800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:228274600-228278800	Enhancers	Placenta Amnion	Placenta Amnion
26	chr1:228274600-228280600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:228274800-228278800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
28	chr1:228274800-228279200	Genic enhancers	Fetal Intestine Large	intestine
29	chr1:228275200-228280800	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:228275200-228282000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:228275400-228278200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:228275400-228279200	Genic enhancers	Fetal Muscle Trunk	muscle
33	chr1:228275400-228281200	Genic enhancers	Gastric	stomach
34	chr1:228275400-228281400	Genic enhancers	Primary B cells from peripheral blood	blood
35	chr1:228275600-228277800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:228275600-228277800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr1:228275600-228278200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
38	chr1:228275600-228279200	Genic enhancers	Thymus	Thymus
39	chr1:228275600-228279400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
40	chr1:228275600-228280200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:228275600-228281200	Genic enhancers	Primary T cells fromperipheralblood	blood
42	chr1:228275800-228277800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:228275800-228278000	Genic enhancers	Spleen	Spleen
44	chr1:228275800-228278800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:228275800-228279400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:228275800-228279400	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
47	chr1:228275800-228279800	Enhancers	Primary hematopoietic stem cells	blood
48	chr1:228275800-228280000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:228275800-228280200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:228275800-228281000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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