Variant report

Variant	rs10136972
Chromosome Location	chr14:55370285-55370286
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	CTCF	chr14:55369349-55370298	K562	blood:	n/a	chr14:55370049-55370067 chr14:55369674-55369683 chr14:55369671-55369689
2	NR2F2	chr14:55368519-55370351	MCF-7	breast:	n/a	n/a
3	ELF1	chr14:55368360-55370452	MCF-7	breast:	n/a	chr14:55369656-55369668
4	POLR2A	chr14:55368605-55370294	HepG2	liver:	n/a	n/a
5	ZEB1	chr14:55368491-55370297	GM12878	blood:	n/a	n/a
6	HDAC2	chr14:55368088-55370292	MCF-7	breast:	n/a	n/a
7	POLR2A	chr14:55370273-55370310	K562	blood:	n/a	n/a
8	CTCF	chr14:55370242-55370290	GM13977	blood:	n/a	n/a
9	MXI1	chr14:55367101-55370353	SK-N-SH	brain:	n/a	chr14:55370063-55370072
10	REST	chr14:55369038-55370346	H1-neurons	neurons:	n/a	n/a
11	CTCF	chr14:55369400-55370370	MCF-7	breast:	n/a	chr14:55370049-55370067 chr14:55369674-55369683 chr14:55369671-55369689
12	NR2F2	chr14:55369244-55370288	MCF-7	breast:	n/a	n/a
13	SIN3AK20	chr14:55368245-55370460	MCF-7	breast:	n/a	n/a
14	RAD21	chr14:55369504-55370287	H1-hESC	embryonic stem cell:	n/a	chr14:55370056-55370065 chr14:55369877-55369889 chr14:55370065-55370077
15	CTCF	chr14:55369457-55370415	HCT-116	colon:	n/a	chr14:55370049-55370067 chr14:55369674-55369683 chr14:55369671-55369689
16	MAX	chr14:55368327-55370467	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:55368751..55370631-chr14:55518308..55520538,2	K562	blood:
2	chr14:55368311..55371330-chr14:55594542..55598408,4	MCF-7	breast:
3	chr14:55030801..55036234-chr14:55366700..55372024,9	MCF-7	breast:
4	chr14:55343213..55346860-chr14:55368496..55370471,3	MCF-7	breast:
5	chr14:55247890..55252413-chr14:55368163..55370491,5	MCF-7	breast:
6	chr14:55351951..55354870-chr14:55368126..55370512,5	MCF-7	breast:
7	chr14:55367425..55371142-chr14:55516489..55521777,7	MCF-7	breast:
8	chr14:55368105..55371463-chr14:55516987..55520396,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SAMD4A-3	chr14:55369024-55370518	NONHSAT036977

Variant related genes	Relation type
GCH1	TF binding region
ENSG00000265432	Chromatin interaction
ENSG00000168175	Chromatin interaction
ENSG00000020577	Chromatin interaction
ENSG00000131981	Chromatin interaction
ENSG00000258872	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10137071	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10140164	0.87[ASN][1000 genomes]
rs10149103	0.86[ASN][1000 genomes]
rs10150110	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1107960	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11158026	0.84[EUR][1000 genomes]
rs11158028	0.86[ASN][1000 genomes]
rs11621165	0.86[ASN][1000 genomes]
rs11621177	0.86[ASN][1000 genomes]
rs11626396	0.86[ASN][1000 genomes]
rs11628304	0.82[AMR][1000 genomes]
rs11846809	0.91[ASN][1000 genomes]
rs11852045	0.84[ASN][1000 genomes]
rs12147796	0.86[ASN][1000 genomes]
rs17832269	0.80[ASN][1000 genomes]
rs2149482	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183085	0.81[EUR][1000 genomes]
rs2840268	0.81[EUR][1000 genomes]
rs28481699	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3759664	0.82[ASN][1000 genomes]
rs3759665	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3783640	0.82[EUR][1000 genomes]
rs3783642	0.92[AFR][1000 genomes]
rs3783643	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3783644	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56164809	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56206440	0.82[EUR][1000 genomes]
rs60258834	0.82[ASN][1000 genomes]
rs61224609	0.88[ASN][1000 genomes]
rs6572993	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6572994	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7146285	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7147286	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7152033	0.89[ASN][1000 genomes]
rs7157085	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7159933	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72715573	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73280573	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8005471	0.82[AMR][1000 genomes]
rs8006363	0.84[ASN][1000 genomes]
rs8007267	0.86[ASN][1000 genomes]
rs8008858	0.85[ASN][1000 genomes]
rs8009997	0.80[ASN][1000 genomes]
rs8011446	0.80[ASN][1000 genomes]
rs8012152	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8013521	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8018688	0.82[ASN][1000 genomes]
rs8018800	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8019220	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8019390	0.86[ASN][1000 genomes]
rs8019824	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8021303	0.82[ASN][1000 genomes]
rs8022453	0.84[ASN][1000 genomes]
rs8023187	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9285583	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9805952	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530042	chr14:55208170-55386966	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS 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 miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv932970	chr14:55326559-55532749	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv3358123	chr14:55359251-55378030	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
4	esv3345259	chr14:55368427-55370975	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55368200-55370400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
2	chr14:55368800-55370400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr14:55369600-55370400	Flanking Active TSS	Dnd41	blood
4	chr14:55369600-55370400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr14:55369800-55370400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr14:55369800-55370400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr14:55370000-55370400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
8	chr14:55370000-55370400	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr14:55370000-55370400	Enhancers	Placenta	Placenta
10	chr14:55370000-55370600	Flanking Active TSS	HepG2	liver
11	chr14:55370000-55373600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr14:55370200-55370400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
13	chr14:55370200-55370400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr14:55370200-55370400	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr14:55370200-55370400	Enhancers	Primary B cells from peripheral blood	blood
16	chr14:55370200-55370400	Enhancers	Primary T cells fromperipheralblood	blood
17	chr14:55370200-55370400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr14:55370200-55370400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr14:55370200-55370400	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr14:55370200-55370400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr14:55370200-55370400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr14:55370200-55370400	Enhancers	Liver	Liver
23	chr14:55370200-55370400	Enhancers	Duodenum Mucosa	Duodenum
24	chr14:55370200-55370400	Flanking Active TSS	Fetal Intestine Small	intestine
25	chr14:55370200-55370400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr14:55370200-55370400	Bivalent Enhancer	Fetal Muscle Leg	muscle
27	chr14:55370200-55370400	Enhancers	Fetal Thymus	thymus
28	chr14:55370200-55370400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr14:55370200-55370400	Enhancers	Thymus	Thymus
30	chr14:55370200-55370400	Flanking Active TSS	Hela-S3	cervix
31	chr14:55370200-55370600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr14:55370200-55372800	Weak transcription	GM12878-XiMat	blood
33	chr14:55370200-55374600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr14:55370200-55374800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr14:55370200-55376800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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