Variant report

Variant	rs28468623
Chromosome Location	chr7:98922812-98922813
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	MAX	chr7:98922784-98923978	K562	blood:	n/a	chr7:98923777-98923787
2	POLR2A	chr7:98922765-98924124	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:98922786-98923827	GM19099	blood:	n/a	n/a
4	POLR2A	chr7:98922550-98923073	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr7:98922203-98924097	K562	blood:	n/a	n/a
6	YY1	chr7:98922649-98923740	H1-hESC	embryonic stem cell:	n/a	chr7:98922977-98922999 chr7:98923723-98923732 chr7:98922976-98922988 chr7:98922980-98922988 chr7:98923083-98923092 chr7:98922975-98922994
7	POLR2A	chr7:98922761-98924742	GM12891	blood:	n/a	n/a
8	POLR2A	chr7:98922710-98924003	U87	brain:	n/a	n/a
9	POLR2A	chr7:98922768-98924045	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr7:98922656-98922957	HCT-116	colon:	n/a	n/a
11	POLR2A	chr7:98921519-98924152	SK-N-MC	brain:	n/a	n/a
12	NRF1	chr7:98922667-98924268	SK-N-SH	brain:	n/a	chr7:98923445-98923456 chr7:98923478-98923489 chr7:98923443-98923457 chr7:98923478-98923487 chr7:98923446-98923457 chr7:98923477-98923488 chr7:98923448-98923457 chr7:98923478-98923492 chr7:98923475-98923489 chr7:98923779-98923788 chr7:98923446-98923460 chr7:98923536-98923545 chr7:98923446-98923455
13	YY1	chr7:98922787-98923820	SK-N-SH_RA	brain:	n/a	chr7:98922977-98922999 chr7:98923723-98923732 chr7:98922976-98922988 chr7:98923779-98923788 chr7:98922980-98922988 chr7:98923083-98923092 chr7:98922975-98922994
14	CHD1	chr7:98922783-98924816	IMR90	lung:	n/a	n/a
15	POLR2A	chr7:98921734-98924171	HepG2	liver:	n/a	n/a
16	POLR2A	chr7:98922666-98924250	K562	blood:	n/a	n/a
17	ZBTB7A	chr7:98922788-98923277	K562	blood:	n/a	n/a
18	JUN	chr7:98922159-98924851	K562	blood:	n/a	chr7:98924136-98924143 chr7:98922377-98922386
19	YY1	chr7:98922792-98923093	HepG2	liver:	n/a	chr7:98922977-98922999 chr7:98922976-98922988 chr7:98922980-98922988 chr7:98923083-98923092 chr7:98922975-98922994
20	POLR2A	chr7:98922772-98923963	GM12892	blood:	n/a	n/a
21	MTA3	chr7:98922633-98924256	GM12878	blood:	n/a	n/a
22	ZNF263	chr7:98922690-98924071	HEK293-T-REx	kidney:	n/a	n/a
23	POLR2A	chr7:98922800-98923811	HEK293	kidney:	n/a	n/a
24	YY1	chr7:98922799-98923835	ECC-1	luminal epithelium:	n/a	chr7:98922977-98922999 chr7:98923723-98923732 chr7:98922976-98922988 chr7:98923779-98923788 chr7:98922980-98922988 chr7:98923083-98923092 chr7:98922975-98922994
25	YY1	chr7:98922714-98923980	HepG2	liver:	n/a	chr7:98922977-98922999 chr7:98923723-98923732 chr7:98922976-98922988 chr7:98923779-98923788 chr7:98922980-98922988 chr7:98923083-98923092 chr7:98922975-98922994
26	MAX	chr7:98922789-98923830	SK-N-SH	brain:	n/a	chr7:98923777-98923787
27	YY1	chr7:98922798-98923112	K562	blood:	n/a	chr7:98922977-98922999 chr7:98922976-98922988 chr7:98922980-98922988 chr7:98923083-98923092 chr7:98922975-98922994
28	POLR2A	chr7:98922804-98924125	Raji	blood:	n/a	n/a
29	POLR2A	chr7:98922718-98924007	H1-hESC	embryonic stem cell:	n/a	n/a
30	HCFC1	chr7:98922686-98924797	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr7:98922440-98923891	PANC-1	pancreas:	n/a	n/a
32	TCF12	chr7:98922796-98924097	A549	lung:	n/a	chr7:98922972-98922982
33	POLR2A	chr7:98922704-98924711	MCF10A-Er-Src	breast:	n/a	n/a
34	REST	chr7:98922701-98924102	H1-neurons	neurons:	n/a	chr7:98923076-98923089
35	MXI1	chr7:98922576-98924856	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr7:98922792-98923997	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr7:98922496-98924096	K562	blood:	n/a	n/a
38	NR2F2	chr7:98922536-98924164	K562	blood:	n/a	n/a
39	POLR2A	chr7:98922616-98923929	MCF-7	breast:	n/a	n/a
40	YY1	chr7:98922652-98923128	GM12878	blood:	n/a	chr7:98922977-98922999 chr7:98922976-98922988 chr7:98922980-98922988 chr7:98923083-98923092 chr7:98922975-98922994
41	YY1	chr7:98922749-98923721	SK-N-SH_RA	brain:	n/a	chr7:98922977-98922999 chr7:98922976-98922988 chr7:98922980-98922988 chr7:98923083-98923092 chr7:98922975-98922994
42	POLR2A	chr7:98922544-98923871	MCF-7	breast:	n/a	n/a
43	ZBTB7A	chr7:98922808-98924015	K562	blood:	n/a	n/a
44	POLR2A	chr7:98922028-98923872	PFSK-1	brain:	n/a	n/a
45	YY1	chr7:98922767-98923148	H1-hESC	embryonic stem cell:	n/a	chr7:98922977-98922999 chr7:98922976-98922988 chr7:98922980-98922988 chr7:98923083-98923092 chr7:98922975-98922994
46	POLR2A	chr7:98922781-98924171	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr7:98922648-98924026	K562	blood:	n/a	n/a
48	BCL3	chr7:98922791-98923786	A549	lung:	n/a	chr7:98923079-98923092 chr7:98923590-98923599 chr7:98923495-98923504 chr7:98923087-98923096
49	YY1	chr7:98922787-98923130	A549	lung:	n/a	chr7:98922977-98922999 chr7:98922976-98922988 chr7:98922980-98922988 chr7:98923083-98923092 chr7:98922975-98922994
50	TAF1	chr7:98922764-98923796	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:98912362..98913995-chr7:98921766..98923287,2	MCF-7	breast:
2	chr7:98922130..98924896-chr7:98987117..98989793,2	K562	blood:
3	chr7:98921655..98927239-chr7:98969297..98973851,7	MCF-7	breast:
4	chr7:98739614..98743126-chr7:98922770..98926033,5	MCF-7	breast:
5	chr7:98921250..98923226-chr7:98924796..98927676,2	MCF-7	breast:
6	chr7:98921987..98924595-chr7:99004669..99006776,2	K562	blood:

Variant related genes	Relation type
ARPC1A	TF binding region
ENSG00000198742	Chromatin interaction
ENSG00000106245	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000130429	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10232076	0.99[ASN][1000 genomes]
rs10255399	0.81[ASN][1000 genomes]
rs10258757	0.81[ASN][1000 genomes]
rs10267346	0.89[ASN][1000 genomes]
rs10272998	0.99[ASN][1000 genomes]
rs10274407	0.99[ASN][1000 genomes]
rs10953287	0.99[ASN][1000 genomes]
rs17161677	0.80[ASN][1000 genomes]
rs17161692	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286162	0.98[ASN][1000 genomes]
rs2301889	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28820905	0.85[ASN][1000 genomes]
rs3779354	0.90[EUR][1000 genomes]
rs3801288	0.98[ASN][1000 genomes]
rs58660994	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59725656	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6948775	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6953476	0.99[ASN][1000 genomes]
rs6972337	0.99[ASN][1000 genomes]
rs6975099	0.99[ASN][1000 genomes]
rs73395547	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73395557	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73395580	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9641253	0.98[ASN][1000 genomes]
rs9768020	0.89[ASN][1000 genomes]
rs9918551	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98908400-98923000	Weak transcription	Aorta	Aorta
2	chr7:98922200-98923200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr7:98922200-98924800	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr7:98922400-98923000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr7:98922400-98923000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:98922400-98923000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr7:98922400-98923000	Flanking Active TSS	Fetal Intestine Small	intestine
8	chr7:98922400-98923000	Flanking Active TSS	Dnd41	blood
9	chr7:98922400-98923200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr7:98922400-98923200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr7:98922400-98923400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr7:98922400-98924200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr7:98922400-98924200	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr7:98922400-98924400	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr7:98922400-98924400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr7:98922400-98924600	Active TSS	GM12878-XiMat	blood
17	chr7:98922400-98924800	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr7:98922400-98924800	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr7:98922400-98925000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:98922400-98925000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:98922600-98923000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:98922600-98923000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr7:98922600-98923000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:98922600-98923000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:98922600-98923000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr7:98922600-98923000	Flanking Active TSS	Fetal Intestine Large	intestine
27	chr7:98922600-98923000	Enhancers	Gastric	stomach
28	chr7:98922600-98923000	Enhancers	Lung	lung
29	chr7:98922600-98923000	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr7:98922600-98923000	Enhancers	Small Intestine	intestine
31	chr7:98922600-98923000	Flanking Active TSS	HMEC	breast
32	chr7:98922600-98923200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr7:98922600-98923200	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr7:98922600-98923200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr7:98922600-98923200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr7:98922600-98923200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:98922600-98923200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr7:98922600-98923200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr7:98922600-98923200	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr7:98922600-98923200	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr7:98922600-98923200	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr7:98922600-98923200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr7:98922600-98923200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr7:98922600-98923200	Flanking Active TSS	Fetal Brain Female	brain
45	chr7:98922600-98923200	Flanking Active TSS	Fetal Muscle Trunk	muscle
46	chr7:98922600-98923200	Flanking Active TSS	Fetal Muscle Leg	muscle
47	chr7:98922600-98923200	Flanking Active TSS	Fetal Stomach	stomach
48	chr7:98922600-98923200	Flanking Active TSS	Right Ventricle	heart
49	chr7:98922600-98923200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr7:98922600-98923200	Flanking Active TSS	Stomach Mucosa	stomach

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