Variant report

Variant	rs58769447
Chromosome Location	chr7:8011974-8011975
allele	-/GC
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	chr7:8007164-8012302	GM12878	blood:	n/a	n/a
2	USF2	chr7:8011822-8012069	GM12878	blood:	n/a	chr7:8011838-8011854
3	CTCF	chr7:8011736-8012100	GM12878	blood:	n/a	n/a
4	MXI1	chr7:8006814-8014285	SK-N-SH	brain:	n/a	n/a
5	RCOR1	chr7:8011176-8011995	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr7:8011661-8012188	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr7:8011704-8012117	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr7:8006896-8012163	GM12891	blood:	n/a	n/a
9	CHD1	chr7:8007292-8013431	GM12878	blood:	n/a	chr7:8008401-8008411 chr7:8008924-8008934 chr7:8008931-8008941 chr7:8008787-8008797
10	MAX	chr7:8011700-8012095	Hela-S3	cervix:	n/a	n/a
11	MAZ	chr7:8011848-8012229	GM12878	blood:	n/a	n/a
12	ZNF263	chr7:8007831-8012241	HEK293-T-REx	kidney:	n/a	chr7:8011925-8011934 chr7:8008196-8008205 chr7:8011226-8011235 chr7:8008843-8008852 chr7:8010817-8010826
13	BCLAF1	chr7:8011680-8012170	GM12878	blood:	n/a	n/a
14	POLR2A	chr7:8011000-8012153	GM12891	blood:	n/a	n/a
15	HCFC1	chr7:8011917-8012037	K562	blood:	n/a	n/a
16	POLR2A	chr7:8006815-8012265	GM12892	blood:	n/a	n/a
17	EP300	chr7:8011841-8012026	GM12878	blood:	n/a	n/a
18	NFATC1	chr7:8010296-8012191	GM12878	blood:	n/a	n/a
19	POLR2A	chr7:8011823-8012037	GM12878	blood:	n/a	n/a
20	YY1	chr7:8011635-8012092	SK-N-SH_RA	brain:	n/a	n/a
21	POLR2A	chr7:8006934-8012236	GM18505	blood:	n/a	n/a
22	POLR2A	chr7:8006829-8012192	GM12892	blood:	n/a	n/a
23	POLR2A	chr7:8011717-8012072	GM12891	blood:	n/a	n/a
24	POLR2A	chr7:8011764-8012190	GM12891	blood:	n/a	n/a
25	BHLHE40	chr7:8011810-8012104	GM12878	blood:	n/a	chr7:8011838-8011854
26	SIN3AK20	chr7:8011701-8012062	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr7:8011714-8012151	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr7:8011859-8012147	Hela-S3	cervix:	n/a	n/a
29	SMC3	chr7:8011639-8012123	GM12878	blood:	n/a	n/a
30	POLR2A	chr7:8006998-8013228	GM12878	blood:	n/a	n/a
31	POLR2A	chr7:8011949-8011983	MCF-7	breast:	n/a	n/a
32	POLR2A	chr7:8010038-8012279	GM12892	blood:	n/a	n/a
33	MAX	chr7:8011824-8012019	GM12878	blood:	n/a	n/a
34	POLR2A	chr7:8011769-8011976	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr7:8011726-8012191	H1-neurons	neurons:	n/a	n/a
36	WRNIP1	chr7:8010182-8012111	GM12878	blood:	n/a	n/a
37	EP300	chr7:8011884-8012006	GM12878	blood:	n/a	n/a
38	BCLAF1	chr7:8011722-8012154	GM12878	blood:	n/a	n/a
39	SIN3A	chr7:8011802-8012054	GM12878	blood:	n/a	n/a
40	POLR2A	chr7:8010995-8012107	GM12891	blood:	n/a	n/a
41	POLR2A	chr7:8006897-8012170	GM12878	blood:	n/a	n/a
42	CHD2	chr7:8011756-8012160	GM12878	blood:	n/a	n/a
43	TBL1XR1	chr7:8011652-8012119	GM12878	blood:	n/a	n/a
44	MXI1	chr7:8011934-8012042	H1-hESC	embryonic stem cell:	n/a	n/a
45	TBP	chr7:8011711-8012138	GM12878	blood:	n/a	n/a
46	POLR2A	chr7:8007791-8012120	Hela-S3	cervix:	n/a	n/a
47	SMC3	chr7:8011858-8012106	Hela-S3	cervix:	n/a	n/a
48	REST	chr7:8011159-8012440	H1-neurons	neurons:	n/a	chr7:8011837-8011855
49	TAF1	chr7:8011746-8011996	SK-N-SH	brain:	n/a	n/a
50	RFX5	chr7:8011729-8012081	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:7951350..7953467-chr7:8011566..8014289,2	MCF-7	breast:
2	chr7:8010918..8013023-chr7:8261319..8263548,2	K562	blood:
3	chr7:7807249..7808898-chr7:8010545..8012405,2	MCF-7	breast:
4	chr7:8011102..8012721-chr7:8079223..8080915,2	K562	blood:
5	chr7:7799170..7801738-chr7:8011527..8014249,3	MCF-7	breast:
6	chr7:8010105..8011990-chr7:8023943..8026240,3	MCF-7	breast:
7	chr7:8006834..8014864-chr7:8015250..8023851,23	K562	blood:
8	chr7:7959000..7960788-chr7:8011254..8013968,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233108	TF binding region
ENSG00000233264	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12113109	0.85[ASN][1000 genomes]
rs13222222	0.95[EUR][1000 genomes]
rs13223417	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13223995	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13237185	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13239966	0.95[EUR][1000 genomes]
rs13240739	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13242904	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13245917	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34318095	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34475980	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34783749	0.95[EUR][1000 genomes]
rs34955320	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35044198	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35108922	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35146192	0.90[ASN][1000 genomes]
rs35149843	0.99[ASN][1000 genomes]
rs35171936	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35225784	0.95[EUR][1000 genomes]
rs35240411	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35394048	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35572840	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35627160	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35630009	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36015287	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36022646	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36028057	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6969431	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71533384	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71533385	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71533389	0.95[EUR][1000 genomes]
rs71533390	0.95[EUR][1000 genomes]
rs715377	0.90[ASN][1000 genomes]
rs7793278	0.99[ASN][1000 genomes]
rs7794417	0.84[EUR][1000 genomes]
rs7800750	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7801299	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7807433	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers 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 target site	84 gene(s)	inside rSNPs	diseases
2	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv1030180	chr7:7860424-8059221	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv3346837	chr7:7915187-8068557	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1020161	chr7:7929384-8047553	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8007200-8012600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:8007200-8013400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr7:8007400-8012200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr7:8007400-8012200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:8007600-8012000	Active TSS	Aorta	Aorta
6	chr7:8007800-8012000	Active TSS	Ovary	ovary
7	chr7:8008200-8013400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr7:8009800-8014800	Active TSS	Brain Germinal Matrix	brain
9	chr7:8010000-8012000	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr7:8010000-8012200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:8010000-8016200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:8010000-8016200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:8010200-8012000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr7:8010200-8012000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr7:8010200-8012000	Flanking Active TSS	K562	blood
16	chr7:8010200-8012200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:8010200-8012200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr7:8010200-8012200	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr7:8010200-8012200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr7:8010200-8012400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr7:8010200-8013400	Flanking Active TSS	Dnd41	blood
22	chr7:8010400-8012000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr7:8010400-8012200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr7:8010400-8015600	Weak transcription	Small Intestine	intestine
25	chr7:8010400-8016200	Weak transcription	Left Ventricle	heart
26	chr7:8010600-8012000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr7:8010600-8012000	Active TSS	Rectal Smooth Muscle	rectum
28	chr7:8010600-8012200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr7:8010600-8012200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr7:8010600-8012200	Flanking Active TSS	Brain Anterior Caudate	brain
31	chr7:8010600-8012200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
32	chr7:8010600-8012200	Enhancers	Placenta Amnion	Placenta Amnion
33	chr7:8010600-8012400	Flanking Active TSS	Fetal Thymus	thymus
34	chr7:8010600-8012800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr7:8010600-8012800	Active TSS	Duodenum Mucosa	Duodenum
36	chr7:8010600-8013000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr7:8010600-8014000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr7:8010800-8012000	Enhancers	H9 Cell Line	embryonic stem cell
39	chr7:8010800-8012000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr7:8010800-8012000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr7:8010800-8012200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr7:8010800-8012800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr7:8010800-8012800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:8010800-8013000	Enhancers	Liver	Liver
45	chr7:8010800-8013200	Enhancers	Primary B cells from peripheral blood	blood
46	chr7:8010800-8013400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr7:8010800-8023600	Weak transcription	Psoas Muscle	Psoas
48	chr7:8011000-8012000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr7:8011000-8012000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr7:8011000-8012200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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