Variant report

Variant	rs10270459
Chromosome Location	chr7:98978960-98978961
allele	C/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	chr7:98978773-98979016	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr7:98976820-98979282	GM10847	blood:	n/a	n/a
3	POLR2A	chr7:98976609-98979475	GM12892	blood:	n/a	n/a
4	YY1	chr7:98978431-98979036	GM12891	blood:	n/a	n/a
5	MXI1	chr7:98978625-98979968	SK-N-SH	brain:	n/a	chr7:98979641-98979650
6	MAX	chr7:98978472-98979596	HepG2	liver:	n/a	chr7:98979002-98979012 chr7:98978961-98978968
7	RELA	chr7:98977642-98979100	GM12892	blood:	n/a	chr7:98978712-98978721 chr7:98978712-98978721
8	WRNIP1	chr7:98977552-98979294	GM12878	blood:	n/a	n/a
9	PAX5	chr7:98978428-98979034	GM12878	blood:	n/a	n/a
10	BCL3	chr7:98978499-98979094	GM12878	blood:	n/a	chr7:98978711-98978720
11	MYC	chr7:98978723-98979130	HepG2	liver:	n/a	chr7:98979002-98979012 chr7:98978961-98978968
12	MXI1	chr7:98978176-98979613	HepG2	liver:	n/a	n/a
13	BCLAF1	chr7:98976667-98979159	GM12878	blood:	n/a	chr7:98977376-98977389 chr7:98978711-98978720 chr7:98977373-98977386
14	CTCF	chr7:98978872-98979091	GM19239	blood:	n/a	n/a
15	POLR2A	chr7:98976628-98979715	GM15510	blood:	n/a	n/a
16	MYC	chr7:98978851-98979131	NB4	blood:	n/a	chr7:98979002-98979012 chr7:98978961-98978968
17	IRF4	chr7:98977599-98979082	GM12878	blood:	n/a	n/a
18	MAX	chr7:98978131-98979860	HepG2	liver:	n/a	chr7:98979002-98979012 chr7:98978961-98978968 chr7:98978274-98978283
19	POLR2A	chr7:98978734-98979184	A549	lung:	n/a	n/a
20	EBF1	chr7:98977626-98979171	GM12878	blood:	n/a	n/a
21	POLR2A	chr7:98976592-98979794	GM12891	blood:	n/a	n/a
22	ELF1	chr7:98977482-98979107	GM12878	blood:	n/a	chr7:98977917-98977930
23	ATF2	chr7:98977524-98979199	GM12878	blood:	n/a	n/a
24	POU2F2	chr7:98977544-98979203	GM12891	blood:	n/a	n/a
25	POLR2A	chr7:98978779-98979711	HepG2	liver:	n/a	n/a
26	POLR2A	chr7:98977475-98979823	K562	blood:	n/a	n/a
27	POLR2A	chr7:98978508-98979207	MCF10A-Er-Src	breast:	n/a	n/a
28	ATF2	chr7:98977541-98979087	GM12878	blood:	n/a	n/a
29	POLR2A	chr7:98976610-98979794	GM18505	blood:	n/a	n/a
30	TAF1	chr7:98978368-98979031	GM12891	blood:	n/a	n/a
31	POLR2A	chr7:98977497-98979791	GM12878	blood:	n/a	n/a
32	POLR2A	chr7:98976834-98979870	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr7:98976659-98979619	GM12878	blood:	n/a	n/a
34	STAT5A	chr7:98976702-98980298	GM12878	blood:	n/a	chr7:98979486-98979498 chr7:98979431-98979443
35	FOXM1	chr7:98976546-98979157	GM12878	blood:	n/a	n/a
36	POLR2A	chr7:98977460-98979044	SK-N-MC	brain:	n/a	n/a
37	YY1	chr7:98978459-98978976	GM12891	blood:	n/a	n/a
38	YY1	chr7:98977482-98979050	GM12878	blood:	n/a	chr7:98978172-98978180
39	RELA	chr7:98976638-98979173	GM10847	blood:	n/a	chr7:98978712-98978721 chr7:98978712-98978721
40	POLR2A	chr7:98978333-98979724	HepG2	liver:	n/a	n/a
41	MAZ	chr7:98977536-98979069	GM12878	blood:	n/a	chr7:98978961-98978968 chr7:98978274-98978283
42	RELA	chr7:98977622-98979147	GM15510	blood:	n/a	chr7:98978712-98978721 chr7:98978712-98978721
43	POLR2A	chr7:98977666-98979210	PANC-1	pancreas:	n/a	n/a
44	TBL1XR1	chr7:98976750-98979149	GM12878	blood:	n/a	n/a
45	POLR2A	chr7:98978574-98979346	U87	brain:	n/a	n/a
46	MAX	chr7:98978815-98979286	NB4	blood:	n/a	chr7:98979002-98979012 chr7:98978961-98978968
47	RELA	chr7:98977674-98979268	GM19193	blood:	n/a	chr7:98978712-98978721 chr7:98978712-98978721
48	POLR2A	chr7:98976524-98979851	GM12892	blood:	n/a	n/a
49	ELK1	chr7:98977681-98979078	GM12878	blood:	n/a	n/a
50	POLR2A	chr7:98976590-98979821	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:98976910..98979073-chr7:98989172..98991412,2	MCF-7	breast:
2	chr7:98975447..98980936-chr7:99003746..99008536,8	MCF-7	breast:
3	chr7:98977788..98980375-chr7:98980403..98983687,6	MCF-7	breast:
4	chr7:98977857..98980973-chr7:99035179..99039094,4	MCF-7	breast:
5	chr7:98975439..98979350-chr7:99003635..99008025,5	K562	blood:
6	chr7:98978155..98981581-chr7:99004279..99007902,6	MCF-7	breast:
7	chr7:98978815..98981136-chr7:98984654..98987297,2	MCF-7	breast:
8	chr7:98966478..98969149-chr7:98977868..98979453,2	MCF-7	breast:
9	chr7:98978195..98983060-chr7:98988487..98993755,6	MCF-7	breast:

Variant related genes	Relation type
ARPC1B	TF binding region
ENSG00000106245	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000160917	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000130429	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10155966	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10236149	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10238965	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs10243678	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10244158	0.80[AMR][1000 genomes]
rs10249167	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10255399	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10258757	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10267346	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10270917	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10271049	0.92[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs10272998	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10274407	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10277149	0.82[EUR][1000 genomes]
rs10279308	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs1043466	0.92[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs10953286	1.00[YRI][hapmap]
rs10953287	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11762273	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11771702	0.84[CEU][hapmap]
rs11973460	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11976018	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs11978089	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs12112936	0.84[CEU][hapmap]
rs12113440	0.84[CEU][hapmap]
rs13227795	0.80[AMR][1000 genomes]
rs13240600	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs17161695	0.84[CEU][hapmap]
rs17161698	0.82[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs1980307	0.92[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs1985453	0.83[ASN][1000 genomes]
rs2003499	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs2057905	0.87[ASN][1000 genomes]
rs2057906	0.91[ASN][1000 genomes]
rs2072181	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2107922	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2240384	0.92[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs2269985	0.82[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2272168	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs2280600	0.92[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs2280601	0.92[CEU][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes]
rs2286162	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2404322	0.90[ASN][1000 genomes]
rs2404323	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2404324	0.81[AFR][1000 genomes]
rs28457808	0.81[AFR][1000 genomes]
rs28495024	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28820905	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3137	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs3764815	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs3779354	0.89[JPT][hapmap]
rs3801288	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3843540	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs4729532	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs59986060	0.83[ASN][1000 genomes]
rs6943920	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6953476	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6955490	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs6962772	0.92[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs6972337	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6975099	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs733991	0.83[CEU][hapmap]
rs7794682	0.80[AMR][1000 genomes]
rs7794705	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs883403	0.92[CEU][hapmap];0.80[AMR][1000 genomes]
rs917154	0.91[CEU][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes]
rs9641253	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9768020	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98971000-98990400	Weak transcription	Fetal Kidney	kidney
2	chr7:98973400-98979000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr7:98973400-98979200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr7:98973400-98984000	Weak transcription	Aorta	Aorta
5	chr7:98973400-98984200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:98973400-98984200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:98973400-98984200	Weak transcription	Ovary	ovary
8	chr7:98973400-98984400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr7:98973400-98987400	Weak transcription	Brain Germinal Matrix	brain
10	chr7:98973400-98987800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:98973400-98989800	Weak transcription	Brain Angular Gyrus	brain
12	chr7:98974800-98979800	Strong transcription	Fetal Intestine Small	intestine
13	chr7:98976600-98979000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr7:98976600-98979200	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr7:98976600-98979200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr7:98976600-98979200	Flanking Active TSS	GM12878-XiMat	blood
17	chr7:98976600-98979400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:98976800-98979000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:98976800-98979000	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr7:98976800-98979000	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr7:98976800-98979000	Enhancers	Stomach Mucosa	stomach
22	chr7:98976800-98979200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr7:98976800-98979200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:98976800-98979400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr7:98976800-98979400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr7:98976800-98979800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr7:98977000-98979200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr7:98977000-98979200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:98977000-98979400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr7:98977000-98979600	Genic enhancers	Muscle Satellite Cultured Cells	--
31	chr7:98977000-98979600	Enhancers	Esophagus	oesophagus
32	chr7:98977000-98979800	Enhancers	Fetal Muscle Trunk	muscle
33	chr7:98977200-98979200	Enhancers	Brain Cingulate Gyrus	brain
34	chr7:98977200-98979800	Enhancers	Left Ventricle	heart
35	chr7:98977600-98979000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr7:98977600-98979200	Transcr. at gene 5' and 3'	Dnd41	blood
37	chr7:98977600-98979400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:98977600-98979400	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
39	chr7:98977600-98979600	Enhancers	Fetal Heart	heart
40	chr7:98977600-98979600	Genic enhancers	Gastric	stomach
41	chr7:98977800-98979000	Genic enhancers	NHLF	lung
42	chr7:98977800-98979200	Active TSS	Rectal Smooth Muscle	rectum
43	chr7:98977800-98979200	Genic enhancers	A549	lung
44	chr7:98977800-98979200	Genic enhancers	HSMM	muscle
45	chr7:98977800-98979600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr7:98977800-98979600	Enhancers	Right Atrium	heart
47	chr7:98977800-98979800	Enhancers	Right Ventricle	heart
48	chr7:98977800-98984000	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr7:98977800-98984200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr7:98978000-98979000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle

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