Variant report

Variant	rs1863077
Chromosome Location	chr7:6388469-6388470
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	FOXA2	chr7:6388421-6389108	A549	lung:	n/a	n/a
2	MXI1	chr7:6388247-6388902	GM12878	blood:	n/a	chr7:6388437-6388452
3	POLR2A	chr7:6388270-6388805	HEK293	kidney:	n/a	n/a
4	CREB1	chr7:6388283-6388940	HepG2	liver:	n/a	chr7:6388595-6388608
5	POLR2A	chr7:6388281-6389078	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr7:6388145-6388848	GM15510	blood:	n/a	n/a
7	YY1	chr7:6388130-6388968	GM12878	blood:	n/a	chr7:6388337-6388348 chr7:6388412-6388421 chr7:6388618-6388632 chr7:6388336-6388345 chr7:6388419-6388433 chr7:6388330-6388344 chr7:6388583-6388597
8	POLR2A	chr7:6388175-6388823	HUVEC	blood vessel:	n/a	n/a
9	SMARCB1	chr7:6387920-6388988	Hela-S3	cervix:	n/a	n/a
10	ATF2	chr7:6388437-6388937	H1-hESC	embryonic stem cell:	n/a	chr7:6388596-6388607
11	POLR2A	chr7:6388118-6388832	GM18526	blood:	n/a	n/a
12	TAF1	chr7:6388418-6388918	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr7:6388450-6388684	GM12891	blood:	n/a	n/a
14	EP300	chr7:6388347-6388750	T-47D	breast:	n/a	chr7:6388628-6388644 chr7:6388579-6388595
15	RAD21	chr7:6388385-6388932	SK-N-SH_RA	brain:	n/a	chr7:6388737-6388756
16	MYC	chr7:6388449-6388817	HepG2	liver:	n/a	chr7:6388614-6388623 chr7:6388707-6388716
17	POLR2A	chr7:6388405-6388789	SK-N-MC	brain:	n/a	n/a
18	SP1	chr7:6388419-6388892	H1-hESC	embryonic stem cell:	n/a	chr7:6388637-6388648 chr7:6388638-6388648 chr7:6388704-6388714 chr7:6388638-6388647 chr7:6388637-6388649 chr7:6388639-6388648 chr7:6388637-6388649 chr7:6388638-6388648 chr7:6388638-6388647
19	RCOR1	chr7:6388415-6388955	Hela-S3	cervix:	n/a	n/a
20	SP1	chr7:6388423-6388940	GM12878	blood:	n/a	chr7:6388637-6388648 chr7:6388638-6388648 chr7:6388704-6388714 chr7:6388638-6388647 chr7:6388637-6388649 chr7:6388639-6388648 chr7:6388637-6388649 chr7:6388638-6388648 chr7:6388638-6388647
21	TBP	chr7:6388440-6389013	HepG2	liver:	n/a	n/a
22	POLR2A	chr7:6388308-6388968	K562	blood:	n/a	n/a
23	POLR2A	chr7:6388326-6388991	PFSK-1	brain:	n/a	n/a
24	MYC	chr7:6388406-6388910	MCF-7	breast:	n/a	chr7:6388414-6388424 chr7:6388614-6388623 chr7:6388707-6388716
25	MXI1	chr7:6388461-6388849	K562	blood:	n/a	n/a
26	TBP	chr7:6388360-6388959	H1-hESC	embryonic stem cell:	n/a	n/a
27	CHD2	chr7:6388437-6388914	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr7:6388211-6388916	K562	blood:	n/a	n/a
29	MYC	chr7:6388055-6388960	K562	blood:	n/a	chr7:6388414-6388424 chr7:6388614-6388623 chr7:6388707-6388716
30	FOXM1	chr7:6388364-6389057	GM12878	blood:	n/a	n/a
31	CTCF	chr7:6388462-6388911	H1-hESC	embryonic stem cell:	n/a	chr7:6388739-6388757 chr7:6388741-6388754 chr7:6388734-6388755 chr7:6388740-6388756
32	MAX	chr7:6387905-6388992	K562	blood:	n/a	chr7:6388414-6388424 chr7:6388614-6388623 chr7:6388707-6388716
33	POLR2A	chr7:6388415-6388693	HepG2	liver:	n/a	n/a
34	ZNF263	chr7:6388468-6388887	HEK293-T-REx	kidney:	n/a	n/a
35	POLR2A	chr7:6388210-6388876	GM12878	blood:	n/a	n/a
36	JUND	chr7:6388289-6389012	A549	lung:	n/a	chr7:6388502-6388511 chr7:6388412-6388421 chr7:6388751-6388759 chr7:6388416-6388425 chr7:6388597-6388606 chr7:6388506-6388515
37	E2F6	chr7:6388412-6388785	A549	lung:	n/a	chr7:6388598-6388607 chr7:6388619-6388628 chr7:6388688-6388697 chr7:6388596-6388605 chr7:6388415-6388424
38	HEY1	chr7:6388206-6388860	HepG2	liver:	n/a	chr7:6388598-6388607 chr7:6388334-6388349 chr7:6388616-6388631 chr7:6388504-6388519 chr7:6388596-6388605 chr7:6388627-6388642 chr7:6388500-6388515
39	ATF3	chr7:6388356-6388835	K562	blood:	n/a	chr7:6388594-6388609 chr7:6388598-6388605 chr7:6388595-6388608 chr7:6388595-6388606 chr7:6388595-6388608 chr7:6388596-6388607 chr7:6388598-6388606 chr7:6388596-6388607
40	IRF1	chr7:6388442-6388890	K562	blood:	n/a	chr7:6388635-6388649
41	PAX5	chr7:6388380-6388886	GM12891	blood:	n/a	chr7:6388539-6388548
42	POLR2A	chr7:6388311-6388934	HepG2	liver:	n/a	n/a
43	REST	chr7:6388467-6388889	A549	lung:	n/a	n/a
44	USF1	chr7:6388431-6388981	A549	lung:	n/a	chr7:6388446-6388462
45	MAX	chr7:6387872-6388928	H1-hESC	embryonic stem cell:	n/a	chr7:6388414-6388424 chr7:6388614-6388623 chr7:6388707-6388716
46	MXI1	chr7:6388076-6388981	Hela-S3	cervix:	n/a	chr7:6388437-6388452
47	CREB1	chr7:6388212-6388980	A549	lung:	n/a	chr7:6388595-6388608
48	ZEB1	chr7:6388014-6388938	GM12878	blood:	n/a	n/a
49	ATF2	chr7:6388420-6388909	GM12878	blood:	n/a	chr7:6388596-6388607
50	HMGN3	chr7:6388448-6388951	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6046534..6048837-chr7:6387102..6390061,2	MCF-7	breast:
2	chr10:93169367..93170145-chr7:6388240..6389220,2	Hela-S3	cervix:
3	chr7:6377795..6380161-chr7:6386976..6388780,2	MCF-7	breast:
4	chr7:6097568..6100190-chr7:6387069..6389785,3	MCF-7	breast:
5	chr7:6387247..6388755-chr7:6413232..6415374,2	MCF-7	breast:
6	chr7:6386514..6388780-chr7:6439968..6442713,2	MCF-7	breast:
7	chr7:6120676..6122302-chr7:6388312..6390000,2	MCF-7	breast:

Variant related genes	Relation type
FAM220A	TF binding region
ENSG00000086232	Chromatin interaction
ENSG00000165338	Chromatin interaction
ENSG00000122512	Chromatin interaction
ENSG00000136238	Chromatin interaction
ENSG00000178397	Chromatin interaction
ENSG00000231704	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11976363	0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2689420	0.89[AMR][1000 genomes]
rs4724797	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6971606	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7788220	0.85[AMR][1000 genomes]
rs7799437	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7801921	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7805985	0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription 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 target site	138 gene(s)	inside rSNPs	diseases
3	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
5	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription 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 target site	127 gene(s)	inside rSNPs	diseases
6	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
7	nsv1021037	chr7:6070792-6426966	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv538713	chr7:6070792-6426966	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv530989	chr7:6176729-6438197	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv482829	chr7:6231809-6407606	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
12	nsv497874	chr7:6296768-6614902	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv1025381	chr7:6356704-6409818	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv538716	chr7:6365534-6400845	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS 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
15	esv3375044	chr7:6387252-6389800	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1863077	RAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6386800-6389000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr7:6387200-6388600	Active TSS	Gastric	stomach
3	chr7:6387200-6389000	Active TSS	H1 Cell Line	embryonic stem cell
4	chr7:6387200-6389000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:6387200-6389000	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr7:6387200-6389000	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr7:6387200-6389000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:6387200-6389000	Active TSS	Brain Hippocampus Middle	brain
9	chr7:6387200-6389000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:6387200-6389000	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr7:6387200-6389200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:6387400-6388800	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr7:6387400-6389000	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr7:6387400-6389000	Active TSS	Fetal Brain Female	brain
15	chr7:6387400-6389000	Active TSS	Stomach Smooth Muscle	stomach
16	chr7:6387600-6388600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr7:6387600-6388600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr7:6387600-6388600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr7:6387600-6388600	Active TSS	Fetal Intestine Large	intestine
20	chr7:6387600-6388600	Active TSS	NHEK	skin
21	chr7:6387600-6388800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr7:6387600-6388800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:6387600-6388800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr7:6387600-6388800	Active TSS	Muscle Satellite Cultured Cells	--
25	chr7:6387600-6388800	Active TSS	HMEC	breast
26	chr7:6387600-6389000	Active TSS	H9 Cell Line	embryonic stem cell
27	chr7:6387600-6389000	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr7:6387600-6389000	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr7:6387600-6389000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:6387600-6389000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr7:6387600-6389000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:6387600-6389000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr7:6387600-6389000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr7:6387600-6389000	Active TSS	Brain Angular Gyrus	brain
35	chr7:6387600-6389000	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr7:6387600-6389000	Active TSS	Fetal Stomach	stomach
37	chr7:6387600-6389000	Active TSS	Rectal Smooth Muscle	rectum
38	chr7:6387600-6389000	Active TSS	A549	lung
39	chr7:6387600-6389000	Active TSS	HepG2	liver
40	chr7:6387600-6389000	Active TSS	HSMM	muscle
41	chr7:6387600-6389000	Active TSS	Osteobl	bone
42	chr7:6387600-6389400	Active TSS	Hela-S3	cervix
43	chr7:6387800-6388600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr7:6387800-6388600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:6387800-6388600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr7:6387800-6388600	Active TSS	Esophagus	oesophagus
47	chr7:6387800-6388600	Active TSS	Right Ventricle	heart
48	chr7:6387800-6388600	Active TSS	Small Intestine	intestine
49	chr7:6387800-6388600	Active TSS	NH-A	brain
50	chr7:6387800-6388800	Active TSS	Colon Smooth Muscle	Colon

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