Variant report

Variant	rs12885036
Chromosome Location	chr14:65228594-65228595
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	EP300	chr14:65226747-65231955	SK-N-SH	brain:	n/a	chr14:65229497-65229513 chr14:65231359-65231366 chr14:65228770-65228786 chr14:65231099-65231108
2	CTCF	chr14:65228548-65228623	HUVEC	blood vessel:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
3	CTCF	chr14:65228540-65228690	GM12873	blood:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
4	CTCF	chr14:65228560-65228598	Kidney_OC	kidney:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
5	CTCF	chr14:65228583-65228625	MCF-7	breast:	n/a	n/a
6	REST	chr14:65228455-65229613	A549	lung:	n/a	chr14:65228473-65228481 chr14:65229146-65229159
7	TCF12	chr14:65228254-65229533	ECC-1	luminal epithelium:	n/a	chr14:65228725-65228733 chr14:65229381-65229391 chr14:65229172-65229182 chr14:65228311-65228321
8	CTCF	chr14:65228500-65228650	HCM	heart:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
9	POLR2A	chr14:65228121-65230150	K562	blood:	n/a	n/a
10	CTCF	chr14:65228560-65228710	AG04449	skin:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
11	CTCF	chr14:65228460-65228610	GM12872	blood:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
12	CTCF	chr14:65228520-65228670	AoAF	blood vessel:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
13	CTCF	chr14:65228520-65228670	HVMF	connective:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
14	MXI1	chr14:65228347-65229692	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr14:65228500-65228650	HRE	kidney:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
16	CTCF	chr14:65228560-65228710	GM12865	blood:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
17	ZNF263	chr14:65228550-65229746	HEK293-T-REx	kidney:	n/a	n/a
18	CTCF	chr14:65228520-65228670	GM12874	blood:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
19	MAX	chr14:65228386-65229907	MCF-7	breast:	n/a	n/a
20	CTCF	chr14:65228520-65228670	HCPEpiC	choroid plexus:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
21	CTCF	chr14:65228480-65228630	HCT-116	colon:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
22	CTCF	chr14:65228520-65228670	NHEK	skin:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
23	EP300	chr14:65228528-65229319	Hela-S3	cervix:	n/a	chr14:65228770-65228786
24	CTCF	chr14:65228560-65228710	HEK293	kidney:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
25	CTCF	chr14:65228540-65228690	NHEK	skin:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
26	MAX	chr14:65228436-65229827	Hela-S3	cervix:	n/a	n/a
27	CEBPB	chr14:65228324-65229770	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr14:65228540-65228690	HA-sp	spinal cord:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
29	CTCF	chr14:65228500-65228650	HEK293	kidney:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
30	CTCF	chr14:65228538-65228646	GM12891	blood:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
31	CTCF	chr14:65228499-65228648	GM12878	blood:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
32	NFIC	chr14:65228548-65229459	SK-N-SH	brain:	n/a	chr14:65229217-65229233 chr14:65229217-65229234 chr14:65229120-65229137
33	RCOR1	chr14:65227974-65229796	IMR90	lung:	n/a	n/a
34	RFX5	chr14:65228388-65229866	Hela-S3	cervix:	n/a	chr14:65229161-65229175
35	CTCF	chr14:65228500-65228650	GM06990	blood:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
36	CTCF	chr14:65228580-65228730	HA-sp	spinal cord:	n/a	n/a
37	CTCF	chr14:65228580-65228730	HVMF	connective:	n/a	n/a
38	MAX	chr14:65228278-65230044	A549	lung:	n/a	n/a
39	CTCF	chr14:65228520-65228670	GM12878	blood:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
40	CTCF	chr14:65228480-65228630	SAEC	small airway:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
41	TFAP2A	chr14:65228270-65230119	Hela-S3	cervix:	n/a	chr14:65229778-65229793 chr14:65229563-65229578 chr14:65229781-65229795 chr14:65229781-65229795 chr14:65229441-65229452 chr14:65229783-65229795 chr14:65229783-65229794
42	CTCF	chr14:65228480-65228630	SK-N-SH_RA	brain:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
43	CTCF	chr14:65228520-65228670	HMEC	breast:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
44	SP1	chr14:65228293-65229656	A549	lung:	n/a	chr14:65229056-65229066
45	TBP	chr14:65228393-65229217	Hela-S3	cervix:	n/a	n/a
46	CTCF	chr14:65228480-65228630	HMF	breast:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
47	BCL3	chr14:65228416-65229594	A549	lung:	n/a	chr14:65228768-65228781 chr14:65228417-65228425
48	TCF12	chr14:65228155-65229895	A549	lung:	n/a	chr14:65228725-65228733 chr14:65229381-65229391 chr14:65229172-65229182 chr14:65228311-65228321
49	CTCF	chr14:65228537-65228645	MCF-7	breast:	n/a	chr14:65228572-65228590 chr14:65228567-65228588
50	CTCF	chr14:65228500-65228688	NHEK	skin:	n/a	chr14:65228572-65228590 chr14:65228567-65228588

No.	Distal block	Cell Line	Cell type
1	chr14:65228573..65229471-chr14:65266358..65267017,2	MCF-7	breast:
2	chr14:65195829..65198759-chr14:65228499..65232345,3	MCF-7	breast:
3	chr14:65228105..65228698-chr2:174886879..174887729,2	MCF-7	breast:
4	chr14:65227919..65230155-chr14:65235739..65238455,3	K562	blood:
5	chr14:65222955..65224467-chr14:65226753..65229376,2	K562	blood:
6	chr14:65228571..65230155-chr14:65235739..65238455,2	K562	blood:
7	chr14:65192290..65195649-chr14:65222693..65231374,9	MCF-7	breast:
8	chr14:65168373..65176902-chr14:65220182..65231670,21	MCF-7	breast:
9	chr14:65168335..65178043-chr14:65220677..65234710,31	MCF-7	breast:
10	chr14:65137759..65138752-chr14:65228203..65228779,2	MCF-7	breast:
11	chr14:65221170..65226335-chr14:65227109..65232798,8	MCF-7	breast:
12	chr14:65228067..65229645-chr14:65348002..65349763,2	K562	blood:
13	chr14:64969302..64971888-chr14:65227488..65230502,4	MCF-7	breast:

Variant related genes	Relation type
SPTB	TF binding region
ENSG00000126804	Chromatin interaction
ENSG00000070182	Chromatin interaction
ENSG00000089775	Chromatin interaction
ENSG00000126822	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10129595	0.82[CEU][hapmap]
rs10148978	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12883860	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12884320	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12889768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12892540	1.00[CEU][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs189086	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs229582	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229598	0.87[ASN][1000 genomes]
rs229601	1.00[ASN][1000 genomes]
rs229602	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34132719	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34494653	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34935243	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35621884	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35752616	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	esv1818582	chr14:65172898-65256685	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1035833	chr14:65176371-65246181	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv1801406	chr14:65193725-65264416	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
4	nsv902023	chr14:65200821-65243885	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv902024	chr14:65200821-65244950	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65211200-65228800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr14:65215200-65232400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr14:65219400-65230000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr14:65219800-65228600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr14:65220600-65232200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr14:65220800-65233000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr14:65221200-65228800	Enhancers	HMEC	breast
8	chr14:65221200-65231600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr14:65221200-65231600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr14:65221400-65229800	Enhancers	Pancreas	Pancrea
11	chr14:65221400-65230000	Enhancers	Fetal Intestine Small	intestine
12	chr14:65221400-65231600	Enhancers	Spleen	Spleen
13	chr14:65221400-65232600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr14:65221600-65232400	Enhancers	Fetal Intestine Large	intestine
15	chr14:65221800-65232200	Enhancers	Placenta Amnion	Placenta Amnion
16	chr14:65222000-65229200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr14:65222200-65229600	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr14:65222200-65231600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr14:65222400-65230000	Enhancers	Stomach Mucosa	stomach
20	chr14:65222600-65228800	Enhancers	Duodenum Mucosa	Duodenum
21	chr14:65222600-65231600	Enhancers	Fetal Heart	heart
22	chr14:65223200-65229400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr14:65223200-65229800	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr14:65223400-65229800	Enhancers	Left Ventricle	heart
25	chr14:65223400-65230000	Enhancers	Fetal Muscle Trunk	muscle
26	chr14:65223600-65230200	Weak transcription	Primary T cells from cord blood	blood
27	chr14:65223600-65230600	Enhancers	Right Ventricle	heart
28	chr14:65223600-65231600	Enhancers	Ovary	ovary
29	chr14:65223600-65232200	Enhancers	Fetal Stomach	stomach
30	chr14:65224000-65231400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr14:65224200-65229000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr14:65224600-65228600	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr14:65224600-65228800	Enhancers	Brain Cingulate Gyrus	brain
34	chr14:65224600-65228800	Enhancers	Brain Hippocampus Middle	brain
35	chr14:65224600-65228800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr14:65225200-65228800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr14:65225200-65229200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr14:65225200-65230800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr14:65225200-65231200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr14:65225400-65229200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr14:65225400-65229600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr14:65225600-65228600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr14:65225800-65228800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr14:65226000-65228800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr14:65226200-65228600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr14:65226200-65228800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr14:65226200-65229200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr14:65226400-65228800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr14:65226800-65228800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr14:65227000-65228800	Enhancers	Brain Germinal Matrix	brain

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