Variant report

Variant	rs822732
Chromosome Location	chr1:228271743-228271744
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	chr1:228269815-228272522	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:228271437-228271884	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:228270811-228271889	GM12891	blood:	n/a	n/a
4	CHD1	chr1:228271191-228271770	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:228269198-228271877	GM19193	blood:	n/a	n/a
6	MXI1	chr1:228269786-228272826	IMR90	lung:	n/a	chr1:228269970-228269979
7	CTCF	chr1:228271620-228271770	AG09319	gingival:	n/a	n/a
8	CTCF	chr1:228271620-228271770	HAc	cerebellar:	n/a	n/a
9	CEBPB	chr1:228271668-228272530	K562	blood:	n/a	chr1:228272300-228272313 chr1:228272302-228272313 chr1:228272477-228272488 chr1:228272300-228272311
10	SMARCB1	chr1:228269838-228271805	Hela-S3	cervix:	n/a	n/a
11	YY1	chr1:228271597-228272021	K562	blood:	n/a	n/a
12	CREB1	chr1:228269350-228271910	HepG2	liver:	n/a	chr1:228270390-228270403
13	MAX	chr1:228271682-228272099	H1-hESC	embryonic stem cell:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
14	CTCF	chr1:228271660-228271810	AG04450	lung:	n/a	n/a
15	POLR2A	chr1:228268843-228274035	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:228269867-228272065	HUVEC	blood vessel:	n/a	n/a
17	MYC	chr1:228271688-228272626	MCF10A-Er-Src	breast:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
18	MAX	chr1:228271537-228272602	NB4	blood:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
19	POLR2A	chr1:228269831-228272124	PFSK-1	brain:	n/a	n/a
20	CEBPB	chr1:228271667-228272505	IMR90	lung:	n/a	chr1:228272300-228272313 chr1:228272302-228272313 chr1:228272477-228272488 chr1:228272300-228272311
21	MAX	chr1:228271423-228271967	Hela-S3	cervix:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
22	POLR2A	chr1:228271358-228272331	GM12891	blood:	n/a	n/a
23	POLR2A	chr1:228269951-228271775	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr1:228271660-228271810	NHDF-neo	bronchial:	n/a	n/a
25	MAX	chr1:228271707-228272413	GM12878	blood:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
26	MAFK	chr1:228271582-228271863	HepG2	liver:	n/a	chr1:228271709-228271723 chr1:228271706-228271721 chr1:228271711-228271722 chr1:228271710-228271721 chr1:228271710-228271721 chr1:228271706-228271722 chr1:228271711-228271722
27	POLR2A	chr1:228269191-228271920	GM12878	blood:	n/a	n/a
28	CTCF	chr1:228271600-228271750	A549	lung:	n/a	n/a
29	POLR2A	chr1:228268861-228272292	K562	blood:	n/a	n/a
30	MYC	chr1:228269434-228272362	K562	blood:	n/a	chr1:228271848-228271859 chr1:228269763-228269773 chr1:228269970-228269981 chr1:228271849-228271856 chr1:228270033-228270043 chr1:228269970-228269980 chr1:228269972-228269979
31	POLR2A	chr1:228271632-228272111	PANC-1	pancreas:	n/a	n/a
32	CTCF	chr1:228271619-228271825	K562	blood:	n/a	n/a
33	SIN3AK20	chr1:228269812-228272410	K562	blood:	n/a	n/a
34	TBL1XR1	chr1:228271690-228273696	K562	blood:	n/a	n/a
35	POLR2A	chr1:228269429-228271869	Hela-S3	cervix:	n/a	n/a
36	MYC	chr1:228268849-228272477	K562	blood:	n/a	chr1:228271848-228271859 chr1:228269763-228269773 chr1:228269970-228269981 chr1:228271849-228271856 chr1:228270033-228270043 chr1:228269015-228269031 chr1:228269970-228269980 chr1:228269972-228269979 chr1:228269039-228269048
37	POLR2A	chr1:228269241-228272029	HepG2	liver:	n/a	n/a
38	POLR2A	chr1:228269801-228272179	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr1:228271711-228271779	ProgFib	skin:	n/a	n/a
40	TBP	chr1:228269916-228271896	K562	blood:	n/a	n/a
41	UBTF	chr1:228269404-228271957	K562	blood:	n/a	n/a
42	MXI1	chr1:228268732-228272801	SK-N-SH	brain:	n/a	chr1:228269970-228269979
43	MAFK	chr1:228271487-228272383	IMR90	lung:	n/a	chr1:228271709-228271723 chr1:228271706-228271721 chr1:228271711-228271722 chr1:228271710-228271721 chr1:228271710-228271721 chr1:228271706-228271722 chr1:228271711-228271722
44	POLR2A	chr1:228270010-228271936	H1-hESC	embryonic stem cell:	n/a	n/a
45	MXI1	chr1:228271328-228272199	K562	blood:	n/a	n/a
46	MAX	chr1:228269245-228272380	HepG2	liver:	n/a	chr1:228271848-228271859 chr1:228269763-228269773 chr1:228269970-228269981 chr1:228271849-228271856 chr1:228270033-228270043 chr1:228269970-228269980 chr1:228269972-228269979
47	POLR2A	chr1:228271236-228271809	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr1:228271720-228271870	HMEC	breast:	n/a	n/a
49	MAX	chr1:228270859-228272047	ECC-1	luminal epithelium:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
50	WRNIP1	chr1:228270941-228273725	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228269915..228273320-chr1:228326449..228329096,4	K562	blood:
2	chr1:227921488..227923041-chr1:228269667..228272192,2	MCF-7	breast:
3	chr1:228192379..228197446-chr1:228268248..228273367,9	MCF-7	breast:
4	chr1:228271061..228272928-chr1:228645504..228647273,2	K562	blood:
5	chr1:228269794..228271921-chr1:228327972..228330804,3	MCF-7	breast:
6	chr1:227916348..227918529-chr1:228270679..228272482,2	MCF-7	breast:
7	chr1:228268894..228271778-chr1:228351302..228354925,4	MCF-7	breast:
8	chr1:228269154..228271874-chr1:228360119..228363775,3	K562	blood:
9	chr1:228271073..228272063-chr1:228289733..228290720,3	MCF-7	breast:
10	chr1:228269773..228272364-chr1:228352112..228354622,6	MCF-7	breast:
11	chr1:228269306..228272326-chr1:228326148..228329488,5	MCF-7	breast:
12	chr1:228271007..228273553-chr1:228330538..228333178,2	MCF-7	breast:
13	chr1:228270338..228271968-chr1:228400103..228402238,2	MCF-7	breast:
14	chr1:228266682..228273620-chr1:228293839..228298603,9	MCF-7	breast:
15	chr1:228270141..228272243-chr1:228325927..228327960,2	MCF-7	breast:
16	chr1:228267667..228275106-chr1:228326600..228331394,10	K562	blood:
17	chr1:228270694..228272754-chr8:126441550..126443960,2	MCF-7	breast:
18	chr1:228270474..228272694-chr1:228336357..228338344,2	K562	blood:
19	chr1:228270437..228272083-chr1:228644163..228645827,2	MCF-7	breast:

Variant related genes	Relation type
ARF1	TF binding region
ENSG00000143774	Chromatin interaction
ENSG00000162910	Chromatin interaction
ENSG00000162913	Chromatin interaction
ENSG00000143740	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000198835	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000081692	Chromatin interaction
ENSG00000143793	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000173334	Chromatin interaction
ENSG00000154342	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10916269	0.92[ASW][hapmap];1.00[MEX][hapmap]
rs1771454	0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1771465	0.87[AMR][1000 genomes]
rs1771466	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1771475	0.92[ASW][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap]
rs1934881	0.84[AFR][1000 genomes]
rs1934882	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs2313599	0.81[AFR][1000 genomes]
rs4653535	0.84[AFR][1000 genomes]
rs4653916	0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs6667424	0.81[AFR][1000 genomes]
rs6686210	0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs7534419	0.81[YRI][hapmap]
rs822728	0.92[ASW][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs822729	0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs822730	0.82[AFR][1000 genomes]
rs822731	0.92[ASW][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs822741	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs849750	0.92[ASW][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs947083	0.84[AFR][1000 genomes]
rs947086	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
12	esv3395884	chr1:228269354-228272202	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228269000-228272200	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:228269200-228271800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr1:228269200-228272000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr1:228269200-228272000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:228269200-228272200	Active TSS	Right Atrium	heart
6	chr1:228269200-228272400	Active TSS	NHLF	lung
7	chr1:228269400-228271800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:228269400-228271800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:228269400-228271800	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:228269400-228271800	Active TSS	Fetal Kidney	kidney
11	chr1:228269400-228271800	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:228269400-228272000	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr1:228269400-228272000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:228269400-228272000	Active TSS	NH-A	brain
15	chr1:228269400-228272400	Active TSS	HSMM	muscle
16	chr1:228269400-228272600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:228269600-228271800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:228269600-228271800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:228269600-228271800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:228269600-228271800	Active TSS	Placenta Amnion	Placenta Amnion
21	chr1:228269600-228271800	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr1:228269600-228271800	Active TSS	Spleen	Spleen
23	chr1:228269600-228271800	Bivalent/Poised TSS	HepG2	liver
24	chr1:228269600-228272000	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr1:228269600-228272000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:228269600-228272000	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr1:228269600-228272000	Active TSS	Fetal Intestine Large	intestine
28	chr1:228269600-228272000	Active TSS	Stomach Mucosa	stomach
29	chr1:228269600-228272200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:228269600-228272200	Active TSS	Gastric	stomach
31	chr1:228269600-228272200	Active TSS	Ovary	ovary
32	chr1:228269600-228272200	Active TSS	Small Intestine	intestine
33	chr1:228269600-228272400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:228269600-228272400	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr1:228269600-228272400	Active TSS	Aorta	Aorta
36	chr1:228269600-228272400	Active TSS	HSMMtube	muscle
37	chr1:228269600-228272400	Active TSS	NHDF-Ad	bronchial
38	chr1:228269600-228272600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:228269600-228272600	Active TSS	Lung	lung
40	chr1:228269600-228272600	Active TSS	Psoas Muscle	Psoas
41	chr1:228269800-228272000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:228270200-228271800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:228270200-228272400	Active TSS	Fetal Muscle Trunk	muscle
44	chr1:228270800-228272200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:228271000-228272000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:228271000-228272000	Transcr. at gene 5' and 3'	Fetal Lung	lung
47	chr1:228271000-228272200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:228271000-228272200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr1:228271000-228272800	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr1:228271000-228273000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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