Variant report

Variant	rs4971059
Chromosome Location	chr1:155148781-155148782
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	chr1:155148093-155149693	SK-N-SH	brain:	n/a	chr1:155149262-155149271 chr1:155149261-155149282 chr1:155149264-155149274 chr1:155149285-155149294 chr1:155149260-155149276 chr1:155149259-155149277 chr1:155149262-155149275
2	RAD21	chr1:155148475-155148856	MCF-7	breast:	n/a	chr1:155148747-155148761
3	RAD21	chr1:155148311-155149729	SK-N-SH	brain:	n/a	chr1:155148747-155148761 chr1:155149265-155149277 chr1:155149302-155149314 chr1:155149261-155149270 chr1:155149260-155149279
4	SMC3	chr1:155148721-155150293	SK-N-SH	brain:	n/a	chr1:155149947-155149957 chr1:155149261-155149275 chr1:155149265-155149275 chr1:155149259-155149273 chr1:155149261-155149269
5	CTCF	chr1:155148740-155148890	AG04449	skin:	n/a	n/a
6	CTCF	chr1:155148580-155148810	GM12864	blood:	n/a	n/a
7	RAD21	chr1:155148289-155149716	HCT-116	colon:	n/a	chr1:155148747-155148761 chr1:155149265-155149277 chr1:155149302-155149314 chr1:155149261-155149270 chr1:155149260-155149279
8	CTCF	chr1:155148339-155149824	HCT-116	colon:	n/a	chr1:155149262-155149271 chr1:155149261-155149282 chr1:155149264-155149274 chr1:155149285-155149294 chr1:155149260-155149276 chr1:155149259-155149277 chr1:155149262-155149275
9	GATA3	chr1:155148676-155149038	T-47D	breast:	n/a	chr1:155148828-155148839
10	CTCF	chr1:155148760-155148910	GM12868	blood:	n/a	n/a
11	CTCF	chr1:155148780-155148930	NHEK	skin:	n/a	n/a
12	MAX	chr1:155148372-155150327	MCF-7	breast:	n/a	chr1:155150204-155150213 chr1:155150227-155150236
13	MXI1	chr1:155144639-155149713	SK-N-SH	brain:	n/a	chr1:155146252-155146261 chr1:155146254-155146263 chr1:155146972-155146987 chr1:155146974-155146989 chr1:155146863-155146872
14	CTCF	chr1:155148760-155148910	HMEC	breast:	n/a	n/a
15	CTCF	chr1:155148471-155148801	MCF-7	breast:	n/a	n/a
16	RAD21	chr1:155148361-155148790	H1-hESC	embryonic stem cell:	n/a	chr1:155148747-155148761
17	CTCF	chr1:155148720-155148870	HCM	heart:	n/a	n/a
18	CEBPB	chr1:155148329-155148815	MCF-7	breast:	n/a	chr1:155148556-155148567
19	POLR2A	chr1:155147446-155152948	MCF10A-Er-Src	breast:	n/a	n/a
20	CTCF	chr1:155148303-155148820	MCF-7	breast:	n/a	n/a
21	CTCF	chr1:155148182-155149735	A549	lung:	n/a	chr1:155149262-155149271 chr1:155149261-155149282 chr1:155149264-155149274 chr1:155149285-155149294 chr1:155149260-155149276 chr1:155149259-155149277 chr1:155149262-155149275
22	CTCF	chr1:155148740-155148890	HEEpiC	esophagus:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155143901..155153030-chr1:155191166..155199183,23	MCF-7	breast:
2	chr1:155148758..155149726-chr1:155162834..155163883,7	K562	blood:
3	chr1:155064648..155066932-chr1:155147928..155150182,2	K562	blood:
4	chr1:155148380..155150190-chr1:155292147..155294545,2	MCF-7	breast:
5	chr1:155095314..155110392-chr1:155134312..155151496,72	MCF-7	breast:
6	chr1:155148507..155150033-chr1:155162898..155164095,27	MCF-7	breast:
7	chr1:155148724..155149607-chr1:155231431..155232032,3	MCF-7	breast:
8	chr1:155148301..155150189-chr1:155162933..155164249,12	MCF-7	breast:
9	chr1:155111752..155114583-chr1:155147267..155150123,4	MCF-7	breast:
10	chr1:155140499..155142005-chr1:155147734..155150654,2	K562	blood:
11	chr1:155148495..155149762-chr1:155196236..155196972,5	MCF-7	breast:
12	chr1:155105664..155110180-chr1:155143584..155151850,15	MCF-7	breast:
13	chr1:155148304..155150985-chr1:155195622..155198249,4	K562	blood:
14	chr1:155148003..155149654-chr1:155176101..155177702,10	MCF-7	breast:
15	chr1:155062424..155064059-chr1:155147918..155149990,2	K562	blood:
16	chr1:155094769..155105017-chr1:155135344..155151845,46	MCF-7	breast:
17	chr1:155139568..155140486-chr1:155148663..155149519,2	K562	blood:
18	chr1:155110723..155114225-chr1:155147854..155154401,7	K562	blood:
19	chr1:155146543..155149271-chr1:155213227..155215655,2	K562	blood:
20	chr1:155146416..155150261-chr1:155194777..155198198,7	MCF-7	breast:
21	chr1:155053097..155054666-chr1:155148381..155150762,2	MCF-7	breast:

Variant related genes	Relation type
KRTCAP2	TF binding region
ENSG00000160766	Chromatin interaction
ENSG00000225855	Chromatin interaction
ENSG00000160753	Chromatin interaction
ENSG00000169231	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000116521	Chromatin interaction
ENSG00000177628	Chromatin interaction
ENSG00000179085	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10157801	0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[AMR][1000 genomes]
rs1057941	0.86[ASN][1000 genomes]
rs10908458	0.86[CHB][hapmap]
rs11264333	0.81[AMR][1000 genomes]
rs11264337	0.86[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs11264338	0.86[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap]
rs11264339	0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs11264341	0.81[CHD][hapmap]
rs11799962	0.90[AMR][1000 genomes]
rs12025371	0.86[CHB][hapmap]
rs12028043	0.86[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.89[AMR][1000 genomes]
rs12124306	0.83[AMR][1000 genomes]
rs12127609	0.89[AMR][1000 genomes]
rs12904	0.85[CHB][hapmap];0.81[CHD][hapmap];0.81[AMR][1000 genomes]
rs2066981	0.81[JPT][hapmap]
rs2070803	0.91[ASN][1000 genomes]
rs2075571	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs34257409	0.90[AMR][1000 genomes]
rs3814316	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4072037	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs423144	0.84[ASN][1000 genomes]
rs4246529	0.86[CHB][hapmap];0.81[CHD][hapmap];0.80[AMR][1000 genomes]
rs4276913	0.85[ASW][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.92[AMR][1000 genomes]
rs4276914	0.81[ASN][1000 genomes]
rs4421576	0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4460629	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs4745	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs4971054	0.82[AMR][1000 genomes]
rs4971066	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs4971073	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap]
rs4971076	0.90[AMR][1000 genomes]
rs4971079	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs4971085	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4971088	0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4971089	0.81[ASN][1000 genomes]
rs4971091	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4971093	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971099	0.83[ASN][1000 genomes]
rs4971100	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4971101	0.91[ASN][1000 genomes]
rs7364524	0.90[AMR][1000 genomes]
rs7366775	0.84[ASN][1000 genomes]
rs7556304	0.86[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs914615	0.91[JPT][hapmap]
rs9297	0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[AMR][1000 genomes]
rs9426886	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
3	nsv464084	chr1:155082298-155194980	Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
4	nsv547961	chr1:155082298-155194980	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
5	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	434 gene(s)	inside rSNPs	diseases
6	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
7	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
8	nsv470741	chr1:155115260-155230131	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
9	nsv1010146	chr1:155119096-155201064	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
10	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
11	nsv8447	chr1:155144629-155156937	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
12	nsv831625	chr1:155145634-155313409	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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	407 gene(s)	inside rSNPs	diseases
13	nsv872458	chr1:155146102-155180466	Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	316 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4971059	GBAP1	cis	Artery Tibial	GTEx
rs4971059	MEIS2	trans	lymphoblastoid	seeQTL
rs4971059	MUC1	cis	Whole Blood	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155146400-155148800	Weak transcription	Hela-S3	cervix
2	chr1:155146400-155157600	Weak transcription	Right Atrium	heart
3	chr1:155146600-155149200	Weak transcription	Pancreas	Pancrea
4	chr1:155146600-155163000	Weak transcription	Aorta	Aorta
5	chr1:155146800-155148800	Active TSS	Brain Anterior Caudate	brain
6	chr1:155146800-155148800	Weak transcription	K562	blood
7	chr1:155146800-155150400	Enhancers	GM12878-XiMat	blood
8	chr1:155146800-155150800	Enhancers	Gastric	stomach
9	chr1:155147000-155148800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:155147000-155149000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:155147000-155149600	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr1:155147000-155149600	Enhancers	A549	lung
13	chr1:155147200-155149000	Weak transcription	HSMM	muscle
14	chr1:155147200-155149400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:155147200-155149600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:155147200-155149800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr1:155147400-155149600	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr1:155147400-155149600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:155147400-155149600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:155147400-155149600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:155147600-155148800	Weak transcription	Primary B cells from cord blood	blood
22	chr1:155147600-155149000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:155147600-155149200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:155147600-155149200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr1:155147600-155149200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:155147600-155149200	Weak transcription	Lung	lung
27	chr1:155147600-155149200	Weak transcription	NHEK	skin
28	chr1:155147600-155149600	Enhancers	Primary T cells fromperipheralblood	blood
29	chr1:155147600-155149600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr1:155147600-155149600	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr1:155147600-155149800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:155147600-155149800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:155147600-155151600	Weak transcription	Osteobl	bone
34	chr1:155147600-155157200	Weak transcription	Right Ventricle	heart
35	chr1:155147800-155148800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:155147800-155148800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:155147800-155149000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr1:155147800-155149000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:155147800-155149400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:155147800-155149400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:155147800-155149400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:155147800-155149400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:155147800-155149400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:155147800-155149400	Weak transcription	HMEC	breast
45	chr1:155147800-155149400	Weak transcription	HUVEC	blood vessel
46	chr1:155147800-155149400	Weak transcription	NHLF	lung
47	chr1:155147800-155149600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:155147800-155149800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:155147800-155149800	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:155148000-155148800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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