Variant report

Variant	rs12936794
Chromosome Location	chr17:19912570-19912571
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	CTCF	chr17:19912540-19912690	AG04450	lung:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
2	TAF1	chr17:19912173-19912873	ECC-1	luminal epithelium:	n/a	n/a
3	CTCF	chr17:19912493-19912758	Hela-S3	cervix:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
4	TCF3	chr17:19912473-19913366	GM12878	blood:	n/a	chr17:19912995-19913008 chr17:19912998-19913012 chr17:19912985-19912999 chr17:19913000-19913010
5	TAF1	chr17:19912451-19912842	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr17:19912367-19912817	A549	lung:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
7	CTCF	chr17:19912520-19912670	GM12864	blood:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
8	MAX	chr17:19912500-19912954	K562	blood:	n/a	chr17:19912536-19912546
9	CTCF	chr17:19912560-19912710	HCPEpiC	choroid plexus:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
10	CTCF	chr17:19912560-19912710	GM12873	blood:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
11	POLR2A	chr17:19912346-19913020	PANC-1	pancreas:	n/a	n/a
12	BHLHE40	chr17:19912461-19912794	GM12878	blood:	n/a	chr17:19912563-19912579 chr17:19912536-19912552 chr17:19912532-19912548
13	E2F6	chr17:19912015-19913448	K562	blood:	n/a	chr17:19913343-19913353 chr17:19912136-19912145
14	TCF12	chr17:19912389-19912965	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr17:19912164-19912933	K562	blood:	n/a	n/a
16	CTCF	chr17:19912540-19912690	HEEpiC	esophagus:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
17	BRCA1	chr17:19912511-19912732	HepG2	liver:	n/a	n/a
18	CTCF	chr17:19912540-19912690	SAEC	small airway:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
19	SIN3AK20	chr17:19912337-19912808	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr17:19912560-19912710	HCT-116	colon:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
21	CTCF	chr17:19912560-19912710	WERI-Rb-1	eye:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
22	MAZ	chr17:19911800-19912900	IMR90	lung:	n/a	chr17:19912536-19912546
23	CTCF	chr17:19912423-19912812	GM12891	blood:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
24	MAZ	chr17:19911943-19913953	K562	blood:	n/a	chr17:19912536-19912546
25	CREB1	chr17:19912287-19913110	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr17:19912339-19912761	HCT-116	colon:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
27	WRNIP1	chr17:19912420-19912645	GM12878	blood:	n/a	n/a
28	SIX5	chr17:19912200-19912808	A549	lung:	n/a	chr17:19912585-19912594 chr17:19912583-19912592
29	MAX	chr17:19912415-19913459	ECC-1	luminal epithelium:	n/a	chr17:19912536-19912546
30	SMC3	chr17:19912449-19912799	K562	blood:	n/a	chr17:19912618-19912632 chr17:19912565-19912575
31	SP1	chr17:19912354-19912806	GM12878	blood:	n/a	n/a
32	POLR2A	chr17:19912378-19913426	A549	lung:	n/a	n/a
33	CTCF	chr17:19912540-19912690	HA-sp	spinal cord:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
34	YY1	chr17:19912424-19912865	K562	blood:	n/a	chr17:19912535-19912549 chr17:19912637-19912651
35	CTCF	chr17:19912540-19912690	HMEC	breast:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
36	YY1	chr17:19912327-19912848	H1-hESC	embryonic stem cell:	n/a	chr17:19912535-19912549 chr17:19912637-19912651
37	RAD21	chr17:19912467-19912731	Hela-S3	cervix:	n/a	n/a
38	SIN3AK20	chr17:19911954-19912960	A549	lung:	n/a	n/a
39	CTCF	chr17:19912433-19912824	A549	lung:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
40	CTCF	chr17:19912448-19912787	Gliobla	brain:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
41	CHD2	chr17:19912424-19912857	Hela-S3	cervix:	n/a	n/a
42	ZC3H11A	chr17:19912363-19912697	K562	blood:	n/a	n/a
43	CTCF	chr17:19912520-19912670	NHEK	skin:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
44	CTCF	chr17:19912448-19912814	GM19239	blood:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
45	YY1	chr17:19912365-19912778	GM12891	blood:	n/a	chr17:19912535-19912549 chr17:19912637-19912651
46	CHD2	chr17:19912496-19912737	GM12878	blood:	n/a	n/a
47	CTCF	chr17:19912480-19912630	WI-38	lung:	n/a	chr17:19912619-19912629
48	SIN3AK20	chr17:19912400-19912842	SK-N-SH	brain:	n/a	n/a
49	CTCF	chr17:19912540-19912690	HL-60	blood:	n/a	chr17:19912622-19912631 chr17:19912617-19912633 chr17:19912619-19912629 chr17:19912616-19912634
50	CTCF	chr17:19911508-19914638	A549	lung:	n/a	chr17:19912622-19912631 chr17:19912985-19912998 chr17:19912998-19913011 chr17:19912617-19912633 chr17:19912019-19912028 chr17:19912619-19912629 chr17:19912616-19912634

No.	Distal block	Cell Line	Cell type
1	chr17:19770311..19771954-chr17:19910328..19912594,2	MCF-7	breast:
2	chr17:19879148..19882537-chr17:19911149..19913260,3	MCF-7	breast:
3	chr17:19912162..19913083-chr17:19998469..19999472,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261033	TF binding region
SPECC1	TF binding region
ENSG00000108599	Chromatin interaction
ENSG00000083290	Chromatin interaction
ENSG00000128487	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12449662	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12450857	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12453720	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12944084	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12946508	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17605101	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17668529	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17759041	0.92[AFR][1000 genomes]
rs2108981	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34182788	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34726000	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35254155	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35315252	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35925051	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35979784	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36097967	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3862151	0.92[AFR][1000 genomes]
rs4577147	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4925063	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4925064	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4925071	0.92[AFR][1000 genomes]
rs4925074	0.92[AFR][1000 genomes]
rs56005410	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62066345	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62066346	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62066347	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62066348	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62066349	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62066350	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62066351	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62066352	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62067482	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62067483	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7209653	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9901294	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv3382860	chr17:19894909-19918588	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12936794	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19911600-19913600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr17:19911600-19913800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr17:19911800-19912600	Bivalent/Poised TSS	Colonic Mucosa	Colon
4	chr17:19911800-19912800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr17:19911800-19912800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr17:19911800-19912800	Active TSS	Right Ventricle	heart
7	chr17:19911800-19912800	Active TSS	GM12878-XiMat	blood
8	chr17:19911800-19913000	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr17:19911800-19913200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr17:19911800-19913800	Active TSS	H9 Cell Line	embryonic stem cell
11	chr17:19911800-19913800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr17:19911800-19913800	Active TSS	Brain Substantia Nigra	brain
13	chr17:19911800-19913800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
14	chr17:19911800-19914000	Active TSS	Brain Anterior Caudate	brain
15	chr17:19911800-19914200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr17:19911800-19914600	Active TSS	Brain Angular Gyrus	brain
17	chr17:19912000-19912600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr17:19912000-19912600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
19	chr17:19912000-19912600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
20	chr17:19912000-19912600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr17:19912000-19912600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr17:19912000-19912600	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr17:19912000-19912600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr17:19912000-19912600	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
25	chr17:19912000-19912600	Bivalent/Poised TSS	Fetal Kidney	kidney
26	chr17:19912000-19912600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
27	chr17:19912000-19912600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
28	chr17:19912000-19912600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
29	chr17:19912000-19912600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr17:19912000-19912600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
31	chr17:19912000-19912600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
32	chr17:19912000-19912600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
33	chr17:19912000-19912800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr17:19912000-19912800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr17:19912000-19912800	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr17:19912000-19912800	Flanking Bivalent TSS/Enh	Dnd41	blood
37	chr17:19912000-19913000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr17:19912000-19913000	Active TSS	HSMM	muscle
39	chr17:19912000-19913200	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr17:19912000-19913200	Active TSS	NHDF-Ad	bronchial
41	chr17:19912000-19913400	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr17:19912000-19913400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
43	chr17:19912000-19913400	Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr17:19912000-19913400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
45	chr17:19912000-19913400	Flanking Active TSS	Osteobl	bone
46	chr17:19912000-19913600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr17:19912000-19913600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr17:19912000-19913600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr17:19912000-19913600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr17:19912000-19913600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood

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