Variant report

Variant	rs28385407
Chromosome Location	chr1:75196341-75196342
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	JUND	chr1:75195506-75196457	SK-N-SH	brain:	n/a	chr1:75195864-75195872 chr1:75195863-75195873 chr1:75195864-75195873 chr1:75195862-75195874 chr1:75195863-75195872 chr1:75195862-75195873 chr1:75195864-75195871
2	JUND	chr1:75195465-75196660	SK-N-SH	brain:	n/a	chr1:75195864-75195872 chr1:75195863-75195873 chr1:75195864-75195873 chr1:75195862-75195874 chr1:75195863-75195872 chr1:75195862-75195873 chr1:75195864-75195871
3	GATA3	chr1:75195771-75196378	MCF-7	breast:	n/a	chr1:75195993-75196002 chr1:75195993-75196000 chr1:75195966-75195974 chr1:75195993-75196000 chr1:75195993-75196000 chr1:75195986-75196007
4	JUND	chr1:75195521-75196451	SK-N-SH	brain:	n/a	chr1:75195864-75195872 chr1:75195863-75195873 chr1:75195864-75195873 chr1:75195862-75195874 chr1:75195863-75195872 chr1:75195862-75195873 chr1:75195864-75195871
5	GATA3	chr1:75195358-75196710	SK-N-SH	brain:	n/a	chr1:75195993-75196002 chr1:75195993-75196000 chr1:75195966-75195974 chr1:75195993-75196000 chr1:75195993-75196000 chr1:75195986-75196007
6	NFIC	chr1:75195492-75196421	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr1:75195517-75196397	SK-N-SH	brain:	n/a	n/a
8	EP300	chr1:75195546-75196432	SK-N-SH	brain:	n/a	chr1:75195864-75195873 chr1:75195764-75195772 chr1:75195863-75195872
9	RXRA	chr1:75195574-75196345	SK-N-SH	brain:	n/a	chr1:75195863-75195872 chr1:75195864-75195873
10	MAX	chr1:75195617-75196373	A549	lung:	n/a	chr1:75195864-75195873 chr1:75195863-75195872
11	GATA3	chr1:75195434-75196539	SK-N-SH	brain:	n/a	chr1:75195993-75196002 chr1:75195993-75196000 chr1:75195966-75195974 chr1:75195993-75196000 chr1:75195993-75196000 chr1:75195986-75196007
12	GATA3	chr1:75195494-75196548	A549	lung:	n/a	chr1:75195993-75196002 chr1:75195993-75196000 chr1:75195966-75195974 chr1:75195993-75196000 chr1:75195993-75196000 chr1:75195986-75196007
13	ARID3A	chr1:75195690-75196472	HepG2	liver:	n/a	n/a
14	MEF2A	chr1:75195599-75196367	SK-N-SH	brain:	n/a	chr1:75196280-75196295 chr1:75196276-75196297 chr1:75196251-75196272
15	PBX3	chr1:75195615-75196454	SK-N-SH	brain:	n/a	n/a
16	TEAD4	chr1:75195612-75196441	SK-N-SH	brain:	n/a	n/a
17	RXRA	chr1:75195692-75196394	SK-N-SH	brain:	n/a	chr1:75195863-75195872 chr1:75195864-75195873
18	PBX3	chr1:75195666-75196402	SK-N-SH	brain:	n/a	n/a
19	TEAD4	chr1:75195685-75196429	SK-N-SH	brain:	n/a	n/a
20	TCF12	chr1:75195541-75196350	A549	lung:	n/a	n/a
21	GATA1	chr1:75195543-75196402	K562	blood:	n/a	chr1:75195993-75196002 chr1:75195993-75196000 chr1:75195966-75195974 chr1:75195993-75196000 chr1:75195993-75196000 chr1:75195986-75196007
22	TCF12	chr1:75195441-75196463	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:75195743..75197778-chr1:75197921..75199580,2	MCF-7	breast:
2	chr1:75192924..75196422-chr1:75198121..75200705,3	MCF-7	breast:

Variant related genes	Relation type
TYW3	TF binding region
ENSG00000162623	Chromatin interaction
ENSG00000116791	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11162088	1.00[AMR][1000 genomes]
rs11163178	0.81[AFR][1000 genomes]
rs12058505	1.00[AMR][1000 genomes]
rs12072488	1.00[AMR][1000 genomes]
rs12093842	1.00[AMR][1000 genomes]
rs17096005	1.00[AMR][1000 genomes]
rs28801184	1.00[AMR][1000 genomes]
rs480165	1.00[AMR][1000 genomes]
rs486644	1.00[AMR][1000 genomes]
rs548924	1.00[AMR][1000 genomes]
rs549607	1.00[AMR][1000 genomes]
rs565749	1.00[AMR][1000 genomes]
rs569165	1.00[AMR][1000 genomes]
rs7529734	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9783028	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv830259	chr1:75089177-75241062	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv871152	chr1:75152186-75197533	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
5	esv1851105	chr1:75152186-75302921	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75167000-75197200	Weak transcription	Right Ventricle	heart
2	chr1:75171000-75197200	Weak transcription	Brain Angular Gyrus	brain
3	chr1:75174800-75198000	Weak transcription	Thymus	Thymus
4	chr1:75180400-75197200	Weak transcription	Psoas Muscle	Psoas
5	chr1:75183000-75198400	Weak transcription	Fetal Brain Male	brain
6	chr1:75187400-75197200	Weak transcription	Stomach Mucosa	stomach
7	chr1:75187800-75197200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:75188200-75197200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:75188200-75198000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:75188400-75196800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:75188400-75197200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:75188400-75198000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:75189000-75197200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:75189200-75196400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:75189400-75197200	Weak transcription	Left Ventricle	heart
16	chr1:75189400-75197400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:75189600-75197200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:75189600-75197400	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:75189800-75196800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:75191400-75197200	Weak transcription	Primary T cells from cord blood	blood
21	chr1:75192000-75197200	Weak transcription	Right Atrium	heart
22	chr1:75192200-75196600	Weak transcription	Aorta	Aorta
23	chr1:75192200-75197000	Weak transcription	Fetal Lung	lung
24	chr1:75192200-75197200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:75192200-75197200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:75192200-75197200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:75192200-75197200	Weak transcription	Colonic Mucosa	Colon
28	chr1:75192200-75197200	Weak transcription	Lung	lung
29	chr1:75192200-75197200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:75192200-75197400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:75192200-75197600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:75192200-75197800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:75192200-75198000	Weak transcription	Gastric	stomach
34	chr1:75192400-75196400	Weak transcription	Fetal Stomach	stomach
35	chr1:75192400-75197200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:75192400-75197200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:75192400-75197200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:75192400-75197200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr1:75192400-75197200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:75192400-75197200	Weak transcription	Fetal Muscle Leg	muscle
41	chr1:75192400-75197400	Weak transcription	Spleen	Spleen
42	chr1:75192400-75198000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr1:75192400-75198000	Weak transcription	Fetal Thymus	thymus
44	chr1:75192600-75197600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:75192800-75197600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:75193000-75197200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:75193000-75197200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr1:75193200-75197200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr1:75193200-75197400	Weak transcription	Primary B cells from cord blood	blood
50	chr1:75193800-75196400	Enhancers	Liver	Liver

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