Variant report

Variant	rs10239259
Chromosome Location	chr7:102004952-102004953
allele	C/T
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	chr7:102003676-102005865	GM12892	blood:	n/a	n/a
2	SIN3AK20	chr7:102004878-102005351	HepG2	liver:	n/a	n/a
3	HEY1	chr7:102003721-102005392	K562	blood:	n/a	chr7:102004899-102004908 chr7:102004901-102004910
4	TAF1	chr7:102004032-102005248	HepG2	liver:	n/a	n/a
5	IRF4	chr7:102004694-102005462	GM12878	blood:	n/a	n/a
6	IRF4	chr7:102004770-102005445	GM12878	blood:	n/a	n/a
7	POLR2A	chr7:102003717-102005965	GM12892	blood:	n/a	n/a
8	POLR2A	chr7:102003672-102006664	GM12878	blood:	n/a	n/a
9	POLR2A	chr7:102004767-102004974	HepG2	liver:	n/a	n/a
10	POLR2A	chr7:102004875-102005067	Gliobla	brain:	n/a	n/a
11	HEY1	chr7:102003661-102005459	K562	blood:	n/a	chr7:102004899-102004908 chr7:102004901-102004910
12	MXI1	chr7:102003901-102005398	SK-N-SH	brain:	n/a	n/a
13	TAF1	chr7:102004095-102005154	HepG2	liver:	n/a	n/a
14	POLR2A	chr7:102003634-102005989	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZBTB33	chr7:102004825-102005455	GM12878	blood:	n/a	n/a
16	GABPA	chr7:102004799-102005395	Hela-S3	cervix:	n/a	n/a
17	SIN3AK20	chr7:102004651-102005155	HepG2	liver:	n/a	n/a
18	UBTF	chr7:102004019-102005167	K562	blood:	n/a	n/a
19	POLR2A	chr7:102004095-102005163	A549	lung:	n/a	n/a
20	NR2F2	chr7:102003650-102006024	K562	blood:	n/a	n/a
21	SP1	chr7:102003666-102005434	GM12878	blood:	n/a	n/a
22	POLR2A	chr7:102003702-102006660	GM12891	blood:	n/a	n/a
23	POLR2A	chr7:102003648-102006639	GM12892	blood:	n/a	n/a
24	USF1	chr7:102004856-102005072	HepG2	liver:	n/a	n/a
25	POLR2A	chr7:102004766-102005444	GM12891	blood:	n/a	n/a
26	PAX5	chr7:102004702-102005426	GM12878	blood:	n/a	chr7:102005042-102005061
27	TCF12	chr7:102004567-102005459	GM12878	blood:	n/a	n/a
28	POLR2A	chr7:102004880-102005072	MCF-7	breast:	n/a	n/a
29	POLR2A	chr7:102003663-102006748	GM12878	blood:	n/a	n/a
30	POU2F2	chr7:102003670-102005435	GM12891	blood:	n/a	chr7:102005069-102005081
31	POLR2A	chr7:102004078-102005404	HepG2	liver:	n/a	n/a
32	HEY1	chr7:102004133-102005002	HepG2	liver:	n/a	chr7:102004899-102004908 chr7:102004901-102004910
33	HEY1	chr7:102003669-102005443	HepG2	liver:	n/a	chr7:102004899-102004908 chr7:102004901-102004910
34	JUND	chr7:102004643-102005355	HepG2	liver:	n/a	n/a
35	POLR2A	chr7:102003718-102005482	Hela-S3	cervix:	n/a	n/a
36	POU2F2	chr7:102003744-102005476	GM12891	blood:	n/a	chr7:102005069-102005081
37	POLR2A	chr7:102004869-102005192	H1-hESC	embryonic stem cell:	n/a	n/a
38	SIX5	chr7:102004872-102005397	K562	blood:	n/a	n/a
39	CBX3	chr7:102004854-102005344	K562	blood:	n/a	n/a
40	POLR2A	chr7:102003674-102005474	GM12891	blood:	n/a	n/a
41	SIN3AK20	chr7:102004860-102005164	A549	lung:	n/a	n/a
42	POLR2A	chr7:102004075-102005381	GM12878	blood:	n/a	n/a
43	POLR2A	chr7:102003792-102005209	A549	lung:	n/a	n/a
44	MAZ	chr7:102003932-102005011	IMR90	lung:	n/a	n/a
45	POLR2A	chr7:102003675-102005458	GM12891	blood:	n/a	n/a
46	BCL11A	chr7:102004788-102005191	GM12878	blood:	n/a	n/a
47	RXRA	chr7:102004920-102005122	HepG2	liver:	n/a	n/a
48	POLR2A	chr7:102003785-102005027	U87	brain:	n/a	n/a
49	PAX5	chr7:102004883-102005404	GM12878	blood:	n/a	chr7:102005042-102005061
50	POLR2A	chr7:102003715-102005400	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:101969853..101972657-chr7:102004064..102005598,2	MCF-7	breast:
2	chr7:101927779..101934386-chr7:102001430..102005829,12	MCF-7	breast:

Variant related genes	Relation type
PRKRIP1	TF binding region
ENSG00000160999	Chromatin interaction
ENSG00000170409	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10229997	1.00[AMR][1000 genomes]
rs10233314	1.00[AMR][1000 genomes]
rs10238685	1.00[AMR][1000 genomes]
rs10249883	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10255036	0.82[AFR][1000 genomes]
rs10259907	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10262517	1.00[AMR][1000 genomes]
rs10266580	1.00[AMR][1000 genomes]
rs10278236	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10280149	1.00[AMR][1000 genomes]
rs28629461	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28669211	1.00[AMR][1000 genomes]
rs28672083	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6970836	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758126	chr7:101912320-102005026	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	esv2759548	chr7:101912320-102005026	Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	esv1814780	chr7:101912320-102375950	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	esv1819566	chr7:101912320-102375950	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats 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	61 gene(s)	inside rSNPs	diseases
5	esv1822347	chr7:101912320-102375950	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	esv1825708	chr7:101912320-102375950	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
7	esv1842898	chr7:101912320-102375950	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	esv1847418	chr7:101912320-102375950	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv427798	chr7:101912320-102375950	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS 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	61 gene(s)	inside rSNPs	diseases
10	nsv428182	chr7:101912320-102375950	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
11	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
12	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	76 gene(s)	inside rSNPs	diseases
13	nsv1029079	chr7:101939998-102112371	Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
14	esv1818954	chr7:101957513-102328097	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	esv1828190	chr7:101966669-102439077	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
16	nsv970918	chr7:101967519-102005026	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	esv3352723	chr7:101969387-102005026	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
18	esv3363254	chr7:101969602-102005026	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
19	esv3489128	chr7:101969639-102005026	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
20	esv3489129	chr7:101969639-102005026	Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
21	esv1829377	chr7:101970299-102330884	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
22	nsv831083	chr7:101981005-102295869	Active TSS Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
23	esv1806297	chr7:101981544-102330884	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
24	esv1810415	chr7:101993063-102375950	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer 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	46 gene(s)	inside rSNPs	diseases
25	esv1811751	chr7:101993063-102375950	Enhancers Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
26	esv1829118	chr7:101993063-102375950	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
27	esv1833155	chr7:101993063-102375950	Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102003400-102005400	Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr7:102003600-102005200	Active TSS	Brain Hippocampus Middle	brain
3	chr7:102003600-102005400	Active TSS	Duodenum Mucosa	Duodenum
4	chr7:102003600-102005800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:102003800-102005000	Active TSS	Primary monocytes fromperipheralblood	blood
6	chr7:102003800-102005000	Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr7:102003800-102005000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:102003800-102005000	Active TSS	Adipose Nuclei	Adipose
9	chr7:102003800-102005200	Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr7:102003800-102005200	Active TSS	Primary T cells from cord blood	blood
11	chr7:102003800-102005200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr7:102003800-102005200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr7:102003800-102005200	Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr7:102003800-102005200	Active TSS	Brain Cingulate Gyrus	brain
15	chr7:102003800-102005200	Active TSS	Brain Substantia Nigra	brain
16	chr7:102003800-102005200	Active TSS	Colon Smooth Muscle	Colon
17	chr7:102003800-102005200	Active TSS	Rectal Mucosa Donor 31	rectum
18	chr7:102003800-102005400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr7:102003800-102005400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:102003800-102005400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr7:102003800-102005400	Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr7:102003800-102005400	Active TSS	Liver	Liver
23	chr7:102003800-102005400	Active TSS	Brain Angular Gyrus	brain
24	chr7:102003800-102005400	Active TSS	Brain Anterior Caudate	brain
25	chr7:102003800-102005400	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr7:102003800-102005400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr7:102003800-102005400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr7:102003800-102005400	Active TSS	Fetal Intestine Large	intestine
29	chr7:102003800-102005400	Active TSS	Fetal Intestine Small	intestine
30	chr7:102003800-102005400	Active TSS	Fetal Kidney	kidney
31	chr7:102003800-102005400	Active TSS	Fetal Lung	lung
32	chr7:102003800-102005400	Active TSS	Fetal Muscle Trunk	muscle
33	chr7:102003800-102005400	Active TSS	Placenta	Placenta
34	chr7:102003800-102005400	Active TSS	Fetal Stomach	stomach
35	chr7:102003800-102005400	Active TSS	Left Ventricle	heart
36	chr7:102003800-102005400	Active TSS	Ovary	ovary
37	chr7:102003800-102005400	Active TSS	Pancreas	Pancrea
38	chr7:102003800-102005400	Active TSS	Psoas Muscle	Psoas
39	chr7:102003800-102005400	Active TSS	Rectal Smooth Muscle	rectum
40	chr7:102003800-102005400	Active TSS	Right Atrium	heart
41	chr7:102003800-102005400	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr7:102003800-102005400	Active TSS	Stomach Smooth Muscle	stomach
43	chr7:102003800-102005400	Active TSS	HUVEC	blood vessel
44	chr7:102003800-102005400	Active TSS	Monocytes-CD14+_RO01746	blood
45	chr7:102003800-102005400	Active TSS	NHDF-Ad	bronchial
46	chr7:102003800-102005400	Active TSS	NHEK	skin
47	chr7:102003800-102005400	Active TSS	NHLF	lung
48	chr7:102003800-102005600	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr7:102003800-102005600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr7:102003800-102005600	Active TSS	HUES6 Cell Line	embryonic stem cell

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