Variant report

Variant	rs2288552
Chromosome Location	chr7:128049590-128049591
allele	A/C
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	BHLHE40	chr7:128049253-128050704	K562	blood:	n/a	chr7:128049741-128049757
2	TBL1XR1	chr7:128049291-128049976	K562	blood:	n/a	n/a
3	POLR2A	chr7:128049541-128050440	PFSK-1	brain:	n/a	n/a
4	RCOR1	chr7:128049322-128050610	K562	blood:	n/a	n/a
5	E2F6	chr7:128049521-128050063	K562	blood:	n/a	chr7:128049581-128049590
6	MXI1	chr7:128049513-128050032	K562	blood:	n/a	n/a
7	MAX	chr7:128049250-128050301	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr7:128049409-128050844	A549	lung:	n/a	n/a
9	MAX	chr7:128049457-128050713	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr7:128049444-128050347	K562	blood:	n/a	n/a
11	MXI1	chr7:128049164-128050981	IMR90	lung:	n/a	n/a
12	HA-E2F1	chr7:128049410-128051408	MCF-7	breast:	n/a	chr7:128049581-128049590
13	ZNF263	chr7:128049003-128050762	HEK293-T-REx	kidney:	n/a	n/a
14	MAFK	chr7:128049463-128049897	K562	blood:	n/a	n/a
15	STAT5A	chr7:128049303-128049740	GM12878	blood:	n/a	chr7:128049709-128049721 chr7:128049321-128049333
16	POLR2A	chr7:128049534-128050449	HUVEC	blood vessel:	n/a	n/a
17	MYC	chr7:128048126-128050706	NB4	blood:	n/a	n/a
18	MAX	chr7:128049492-128050879	MCF-7	breast:	n/a	n/a
19	CREB1	chr7:128049590-128050547	A549	lung:	n/a	n/a
20	MAX	chr7:128049409-128049919	GM12878	blood:	n/a	n/a
21	POLR2A	chr7:128049546-128050640	HCT-116	colon:	n/a	n/a
22	E2F6	chr7:128049300-128049992	A549	lung:	n/a	chr7:128049581-128049590
23	UBTF	chr7:128049529-128050631	K562	blood:	n/a	n/a
24	PAX5	chr7:128049543-128050039	GM12892	blood:	n/a	n/a
25	POLR2A	chr7:128049439-128050615	K562	blood:	n/a	n/a
26	GTF2F1	chr7:128049524-128049641	K562	blood:	n/a	n/a
27	YY1	chr7:128049582-128050042	K562	blood:	n/a	chr7:128049763-128049777
28	PML	chr7:128049589-128050456	GM12878	blood:	n/a	n/a
29	STAT3	chr7:128049371-128049781	MCF10A-Er-Src	breast:	n/a	chr7:128049709-128049721
30	EGR1	chr7:128049538-128050287	K562	blood:	n/a	chr7:128049715-128049728 chr7:128049716-128049726 chr7:128049750-128049760
31	STAT3	chr7:128049423-128049888	MCF10A-Er-Src	breast:	n/a	chr7:128049709-128049721
32	YY1	chr7:128049589-128050079	SK-N-SH_RA	brain:	n/a	chr7:128049763-128049777
33	POLR2A	chr7:128048822-128050596	Hela-S3	cervix:	n/a	n/a
34	CCNT2	chr7:128049131-128050582	K562	blood:	n/a	chr7:128049714-128049723
35	NR2F2	chr7:128048091-128050803	K562	blood:	n/a	n/a
36	POLR2A	chr7:128049574-128050120	HUVEC	blood vessel:	n/a	n/a
37	SMARCB1	chr7:128048959-128050565	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr7:128049123-128050702	HL-60	blood:	n/a	n/a
39	POLR2A	chr7:128049148-128050296	K562	blood:	n/a	n/a
40	MAX	chr7:128048182-128050697	NB4	blood:	n/a	n/a
41	E2F6	chr7:128049276-128050016	K562	blood:	n/a	chr7:128049581-128049590
42	E2F6	chr7:128049507-128050206	K562	blood:	n/a	chr7:128049581-128049590
43	POLR2A	chr7:128049085-128050520	K562	blood:	n/a	n/a
44	FOXP2	chr7:128049537-128050083	PFSK-1	brain:	n/a	n/a
45	ZBTB7A	chr7:128049361-128050567	K562	blood:	n/a	n/a
46	YY1	chr7:128049477-128050173	K562	blood:	n/a	chr7:128050110-128050124 chr7:128049763-128049777 chr7:128049579-128049590
47	MAZ	chr7:128048724-128051079	IMR90	lung:	n/a	n/a
48	POLR2A	chr7:128049512-128050755	HCT-116	colon:	n/a	n/a
49	POLR2A	chr7:128049524-128050698	U87	brain:	n/a	n/a
50	POLR2A	chr7:128049338-128050299	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:128048546..128051424-chr8:143807465..143809769,2	MCF-7	breast:
2	chr7:128048293..128050679-chr7:128502108..128504312,2	MCF-7	breast:
3	chr7:127982196..127985036-chr7:128048348..128051893,5	MCF-7	breast:
4	chr7:128047161..128050572-chr7:128094387..128098790,7	K562	blood:
5	chr7:128049014..128051472-chr7:128115731..128117859,3	K562	blood:
6	chr7:128047282..128051646-chr7:128071407..128074955,4	MCF-7	breast:
7	chr7:128049232..128052115-chr7:128095566..128097196,2	MCF-7	breast:
8	chr11:18034017..18034785-chr7:128049172..128050147,2	NB4	blood:
9	chr7:128047161..128050830-chr7:128093884..128097132,5	K562	blood:

Variant related genes	Relation type
IMPDH1	TF binding region
ENSG00000242902	Chromatin interaction
ENSG00000253806	Chromatin interaction
ENSG00000228700	Chromatin interaction
ENSG00000165055	Chromatin interaction
ENSG00000106344	Chromatin interaction
ENSG00000240758	Chromatin interaction
ENSG00000128524	Chromatin interaction
ENSG00000238750	Chromatin interaction
ENSG00000129158	Chromatin interaction
ENSG00000273184	Chromatin interaction
ENSG00000253741	Chromatin interaction
ENSG00000135245	Chromatin interaction
ENSG00000130193	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2288551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288555	0.89[EUR][1000 genomes]
rs2288558	0.92[AMR][1000 genomes]
rs3793166	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4731452	0.98[ASN][1000 genomes]
rs56777177	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57025636	1.00[EUR][1000 genomes]
rs57342587	1.00[EUR][1000 genomes]
rs58116488	1.00[EUR][1000 genomes]
rs58306387	1.00[EUR][1000 genomes]
rs58346994	1.00[EUR][1000 genomes]
rs58432768	1.00[EUR][1000 genomes]
rs59521761	1.00[EUR][1000 genomes]
rs59959624	1.00[EUR][1000 genomes]
rs60041365	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61030579	1.00[EUR][1000 genomes]
rs714510	0.96[ASN][1000 genomes]
rs72624929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831124	chr7:127970345-128147910	Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv889191	chr7:127973133-128073326	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	esv2493565	chr7:127985695-128053377	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	esv3478325	chr7:127986726-128053483	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv3478326	chr7:127986726-128053483	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv515737	chr7:128044035-128050417	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	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	chr7:128046400-128049600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr7:128047600-128049600	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr7:128047800-128050400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:128047800-128051000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:128048000-128049600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:128048000-128049800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr7:128048000-128049800	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr7:128048200-128049600	Flanking Bivalent TSS/Enh	HepG2	liver
9	chr7:128048200-128049800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr7:128048200-128050000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr7:128048400-128049600	Flanking Active TSS	NHEK	skin
12	chr7:128048400-128050800	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr7:128048600-128049600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:128048600-128049600	Flanking Active TSS	Fetal Stomach	stomach
15	chr7:128048600-128049800	Enhancers	Fetal Heart	heart
16	chr7:128048800-128049600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:128048800-128049600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:128048800-128049600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr7:128048800-128049600	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr7:128048800-128049600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
21	chr7:128048800-128049600	Flanking Active TSS	Fetal Muscle Leg	muscle
22	chr7:128048800-128049600	Flanking Active TSS	Right Ventricle	heart
23	chr7:128048800-128049600	Flanking Active TSS	A549	lung
24	chr7:128048800-128049600	Flanking Active TSS	Hela-S3	cervix
25	chr7:128048800-128049600	Flanking Active TSS	NHLF	lung
26	chr7:128048800-128049800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:128048800-128049800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr7:128048800-128049800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr7:128048800-128049800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:128048800-128049800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr7:128048800-128049800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
32	chr7:128048800-128049800	Flanking Active TSS	K562	blood
33	chr7:128049000-128049600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
34	chr7:128049000-128049600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr7:128049000-128049600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
36	chr7:128049000-128049600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
37	chr7:128049000-128049600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
38	chr7:128049000-128049600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr7:128049000-128049600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr7:128049000-128049600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr7:128049000-128049600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr7:128049000-128049600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr7:128049000-128049600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr7:128049000-128049600	Flanking Active TSS	Brain Angular Gyrus	brain
45	chr7:128049000-128049600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr7:128049000-128049600	Flanking Active TSS	Fetal Lung	lung
47	chr7:128049000-128049600	Flanking Active TSS	Placenta	Placenta
48	chr7:128049000-128049600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr7:128049000-128049600	Flanking Active TSS	Spleen	Spleen
50	chr7:128049000-128049600	Flanking Active TSS	HSMMtube	muscle

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