Variant report

Variant	rs550597
Chromosome Location	chr1:153505774-153505775
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	CTCF	chr1:153505700-153505850	HEK293	kidney:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
2	ZBTB7A	chr1:153505538-153506136	ECC-1	luminal epithelium:	n/a	n/a
3	CTCF	chr1:153505680-153505830	GM12873	blood:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
4	POLR2A	chr1:153505618-153506744	A549	lung:	n/a	n/a
5	PBX3	chr1:153505314-153506846	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr1:153505698-153505849	SK-N-SH_RA	brain:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
7	CTCF	chr1:153505643-153505917	GM12878	blood:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
8	TCF12	chr1:153505534-153506114	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr1:153504001-153509011	U87	brain:	n/a	n/a
10	JUND	chr1:153505713-153507187	Hela-S3	cervix:	n/a	chr1:153506973-153506981 chr1:153506973-153506982 chr1:153506972-153506982 chr1:153506399-153506406 chr1:153506396-153506407 chr1:153506974-153506981
11	POLR2A	chr1:153504109-153508508	A549	lung:	n/a	n/a
12	POLR2A	chr1:153505145-153509494	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr1:153505666-153505907	Fibrobl	skin:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
14	SIN3A	chr1:153505296-153506129	H1-hESC	embryonic stem cell:	n/a	n/a
15	E2F6	chr1:153505665-153505849	K562	blood:	n/a	n/a
16	ZBTB33	chr1:153505646-153506696	SK-N-SH	brain:	n/a	n/a
17	CTCF	chr1:153505700-153505850	HA-sp	spinal cord:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
18	CTCF	chr1:153505576-153505966	T-47D	breast:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
19	CTCF	chr1:153505653-153505901	H1-hESC	embryonic stem cell:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
20	CTCF	chr1:153505641-153505907	GM19240	blood:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
21	POLR2A	chr1:153505510-153505910	K562	blood:	n/a	n/a
22	CTCF	chr1:153505628-153505910	Pancreas_OC	pancreas:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
23	SP1	chr1:153505368-153506836	A549	lung:	n/a	chr1:153506427-153506437 chr1:153505389-153505398 chr1:153506427-153506436 chr1:153506428-153506437 chr1:153506693-153506702 chr1:153506427-153506436
24	TFAP2C	chr1:153505386-153507077	Hela-S3	cervix:	n/a	n/a
25	MAX	chr1:153505614-153506819	Hela-S3	cervix:	n/a	chr1:153506458-153506465
26	POLR2A	chr1:153505214-153506163	MCF-7	breast:	n/a	n/a
27	POLR2A	chr1:153505307-153509454	Hela-S3	cervix:	n/a	n/a
28	CEBPB	chr1:153505390-153505977	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr1:153505679-153505899	GM19239	blood:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
30	TAF1	chr1:153505652-153505906	K562	blood:	n/a	n/a
31	CTCF	chr1:153505700-153505850	WERI-Rb-1	eye:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
32	TBL1XR1	chr1:153505680-153505967	K562	blood:	n/a	n/a
33	CTCF	chr1:153505644-153505904	MCF-7	breast:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
34	POLR2A	chr1:153505192-153509569	HCT-116	colon:	n/a	n/a
35	YY1	chr1:153505707-153505846	HCT-116	colon:	n/a	n/a
36	CTCF	chr1:153505720-153505870	GM12864	blood:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
37	CTCF	chr1:153505720-153505870	NHEK	skin:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
38	CTCF	chr1:153505492-153505991	MCF-7	breast:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
39	CTCF	chr1:153505700-153505850	GM12873	blood:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
40	MAZ	chr1:153504643-153509324	IMR90	lung:	n/a	chr1:153506458-153506465 chr1:153508744-153508753 chr1:153506973-153506982 chr1:153509221-153509231 chr1:153506972-153506981 chr1:153509055-153509062 chr1:153508744-153508753
41	MAX	chr1:153505450-153509582	HCT-116	colon:	n/a	chr1:153506458-153506465 chr1:153508744-153508753 chr1:153506973-153506982 chr1:153509221-153509231 chr1:153506972-153506981 chr1:153509055-153509062 chr1:153508744-153508753
42	CHD2	chr1:153505478-153505901	K562	blood:	n/a	n/a
43	NFYA	chr1:153505675-153506550	Hela-S3	cervix:	n/a	n/a
44	CTCF	chr1:153505618-153505904	HepG2	liver:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
45	CTCF	chr1:153505740-153505890	GM12872	blood:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
46	KAT2A	chr1:153505730-153507273	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr1:153505680-153505830	GM12864	blood:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
48	CTCF	chr1:153505569-153505995	K562	blood:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
49	CTCF	chr1:153505563-153505950	A549	lung:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
50	SP1	chr1:153505226-153506047	H1-hESC	embryonic stem cell:	n/a	chr1:153505389-153505398

No.	Distal block	Cell Line	Cell type
1	chr1:153503911..153505890-chr1:153631477..153634216,2	K562	blood:
2	chr1:153505459..153506316-chr6:26199169..26200064,2	Hela-S3	cervix:
3	chr1:153505342..153508148-chr1:153641864..153643367,2	MCF-7	breast:
4	chr1:153504382..153507280-chr1:153522086..153523762,2	K562	blood:
5	chr1:153504897..153511307-chr1:153536318..153542519,37	MCF-7	breast:
6	chr1:153504329..153507150-chr1:153606463..153608211,3	MCF-7	breast:
7	chr1:153504925..153506891-chr1:153507588..153509186,2	K562	blood:
8	chr1:153504456..153510099-chr1:153538941..153542898,8	K562	blood:
9	chr1:153504127..153510657-chr1:153537210..153543304,15	K562	blood:
10	chr1:153504209..153505838-chr1:153511280..153513163,2	K562	blood:
11	chr1:153505312..153506366-chr1:153540363..153541887,16	K562	blood:
12	chr1:153503567..153510701-chr1:153536906..153541884,20	MCF-7	breast:
13	chr1:153505490..153510008-chr1:153584041..153589482,7	MCF-7	breast:
14	chr1:153502325..153505921-chr1:153601540..153604182,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238279	TF binding region
ENSG00000197409	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000189171	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16835393	0.92[CEU][hapmap];0.85[MEX][hapmap];0.80[AMR][1000 genomes]
rs17695220	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs1810765	1.00[JPT][hapmap]
rs1887039	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs2094217	0.84[EUR][1000 genomes]
rs2094737	0.84[EUR][1000 genomes]
rs2094738	0.82[EUR][1000 genomes]
rs2248745	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2262587	0.84[EUR][1000 genomes]
rs2480695	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2480696	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28427870	0.83[ASN][1000 genomes]
rs28483109	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3762262	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4017737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4272569	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs4430277	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs477339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845351	0.92[CEU][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]
rs4845352	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4845552	0.86[GIH][hapmap];0.85[MEX][hapmap]
rs4845554	0.92[CEU][hapmap];0.80[AMR][1000 genomes]
rs532652	0.82[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs552446	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs585215	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6587743	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs6587745	0.80[AMR][1000 genomes]
rs6587746	0.80[AMR][1000 genomes]
rs659403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6684970	0.92[CEU][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap]
rs7518306	0.92[CEU][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9426945	0.84[EUR][1000 genomes]
rs9427239	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9427287	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153489000-153506000	Weak transcription	Gastric	stomach
2	chr1:153498000-153505800	Weak transcription	Aorta	Aorta
3	chr1:153498200-153506000	Weak transcription	Right Ventricle	heart
4	chr1:153503400-153507200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:153503800-153507400	Enhancers	Small Intestine	intestine
6	chr1:153504000-153505800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:153504000-153506400	Enhancers	Primary T cells from cord blood	blood
8	chr1:153504000-153507600	Enhancers	Fetal Thymus	thymus
9	chr1:153504200-153505800	Enhancers	Esophagus	oesophagus
10	chr1:153504200-153506000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:153504200-153506000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:153504200-153506600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr1:153504200-153507600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:153504400-153505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:153504400-153506800	Enhancers	Primary B cells from peripheral blood	blood
16	chr1:153504400-153507000	Enhancers	Primary hematopoietic stem cells	blood
17	chr1:153504600-153505800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:153504600-153506200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr1:153504600-153506200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr1:153504600-153506400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr1:153504800-153505800	Enhancers	Placenta Amnion	Placenta Amnion
22	chr1:153504800-153505800	Enhancers	NHLF	lung
23	chr1:153504800-153506000	Enhancers	HMEC	breast
24	chr1:153504800-153506400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr1:153504800-153506600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:153504800-153507200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr1:153504800-153507200	Enhancers	Spleen	Spleen
28	chr1:153504800-153507800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:153504800-153507800	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr1:153504800-153508000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:153505000-153505800	Enhancers	Adipose Nuclei	Adipose
32	chr1:153505000-153506400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr1:153505000-153506400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:153505000-153506600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:153505000-153506800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:153505000-153507000	Flanking Active TSS	Hela-S3	cervix
37	chr1:153505000-153507400	Enhancers	Liver	Liver
38	chr1:153505200-153505800	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr1:153505200-153505800	Enhancers	Osteobl	bone
40	chr1:153505200-153506000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr1:153505200-153506000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr1:153505200-153506000	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr1:153505200-153506000	Enhancers	Left Ventricle	heart
44	chr1:153505200-153506200	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr1:153505200-153506200	Enhancers	Lung	lung
46	chr1:153505200-153506200	Flanking Active TSS	HSMM	muscle
47	chr1:153505200-153506200	Flanking Active TSS	NHDF-Ad	bronchial
48	chr1:153505200-153506400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:153505200-153506400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr1:153505200-153506600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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