Variant report

Variant	rs4851267
Chromosome Location	chr2:100824104-100824105
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	EP300	chr2:100823765-100824481	SK-N-SH_RA	brain:	n/a	chr2:100824035-100824048
2	RAD21	chr2:100823672-100824122	H1-hESC	embryonic stem cell:	n/a	n/a
3	REST	chr2:100823800-100824408	SK-N-SH	brain:	n/a	n/a
4	RAD21	chr2:100823825-100824334	SK-N-SH_RA	brain:	n/a	n/a
5	GATA3	chr2:100823831-100824560	SK-N-SH	brain:	n/a	chr2:100824507-100824516 chr2:100824370-100824382 chr2:100824368-100824384
6	RAD21	chr2:100823879-100824107	H1-hESC	embryonic stem cell:	n/a	n/a
7	GATA3	chr2:100823900-100824575	SK-N-SH	brain:	n/a	chr2:100824507-100824516 chr2:100824370-100824382 chr2:100824368-100824384
8	EP300	chr2:100821970-100825396	SK-N-SH	brain:	n/a	chr2:100823751-100823765 chr2:100822832-100822841 chr2:100823096-100823110 chr2:100823491-100823505 chr2:100823084-100823098 chr2:100824035-100824048
9	GATA2	chr2:100823102-100825032	SH-SY5Y	brain:	n/a	chr2:100824507-100824516 chr2:100824370-100824382 chr2:100823442-100823451 chr2:100823653-100823663 chr2:100824368-100824384
10	TCF12	chr2:100823745-100824531	SK-N-SH	brain:	n/a	n/a
11	MXI1	chr2:100822357-100824778	SK-N-SH	brain:	n/a	chr2:100824104-100824119 chr2:100824102-100824117
12	EP300	chr2:100823876-100824427	SK-N-SH_RA	brain:	n/a	chr2:100824035-100824048
13	GATA3	chr2:100823136-100824498	SH-SY5Y	brain:	n/a	chr2:100824370-100824382 chr2:100823442-100823451 chr2:100823653-100823663 chr2:100824368-100824384
14	MAX	chr2:100823669-100824298	NB4	blood:	n/a	chr2:100824183-100824193 chr2:100824104-100824113
15	RAD21	chr2:100822638-100825375	SK-N-SH	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:100824103-100824153	SK-N-SH	brain:	n/a
2	chr2:100824103-100824153	T-47D	breast:	n/a
3	chr2:100824103-100824153	AG04450	lung:	fetal
4	chr2:100824103-100824153	Hepatocyte	liver:	n/a
5	chr2:100824103-100824153	U87	brain:	n/a
6	chr2:100824103-100824153	CMK	blood:	n/a
7	chr2:100824103-100824153	MCF-7	breast:	n/a
8	chr2:100824103-100824153	HUVEC	blood vessel:	n/a
9	chr2:100824103-100824153	Caco-2	colon:	n/a
10	chr2:100824103-100824153	HMEC	breast:	n/a
11	chr2:100824103-100824153	NH-A	brain:	n/a
12	chr2:100824103-100824153	HEK293	kidney:	embryo
13	chr2:100824103-100824153	NHDF-neo	bronchial:	n/a
14	chr2:100824103-100824153	H1-hESC	embryonic stem cell:	embryo
15	chr2:100824103-100824153	PrEC	prostate:	n/a
16	chr2:100824103-100824153	HepG2	liver:	n/a
17	chr2:100824103-100824153	HCF	heart:	n/a
18	chr2:100824103-100824153	BE2_C	brain:	n/a
19	chr2:100824103-100824153	ECC-1	luminal epithelium:	n/a
20	chr2:100824103-100824153	HRE	kidney:	n/a
21	chr2:100824103-100824153	HRPEpiC	eye:	n/a
22	chr2:100824103-100824153	ProgFib	skin:	n/a
23	chr2:100824103-100824153	LNCaP	prostate:	n/a
24	chr2:100824103-100824153	HIPEpiC	eye:	n/a
25	chr2:100824103-100824153	HEEpiC	esophagus:	n/a
26	chr2:100824103-100824153	GM06990	blood:	n/a
27	chr2:100824103-100824153	HAEpiC	amniotic membrane:	n/a
28	chr2:100824103-100824153	A549	lung:	n/a
29	chr2:100824103-100824153	GM12892	blood:	n/a
30	chr2:100824103-100824153	AG09309	skin:	n/a
31	chr2:100824103-100824153	RPTEC	kidney:	n/a
32	chr2:100824103-100824153	HL-60	blood:	n/a
33	chr2:100824103-100824153	SK-N-SH_RA	brain:	n/a
34	chr2:100824103-100824153	AG04449	skin:	fetal
35	chr2:100824103-100824153	IMR90	lung:	fetal
36	chr2:100824103-100824153	SAEC	small airway:	n/a
37	chr2:100824103-100824153	MCF10A-Er-Src	breast:	n/a
38	chr2:100824103-100824153	ovcar-3	ovarian:	n/a
39	chr2:100824103-100824153	AG09319	gingival:	n/a
40	chr2:100824103-100824153	NT2-D1	testis:	n/a
41	chr2:100824103-100824153	K562	blood:	n/a
42	chr2:100824103-100824153	Jurkat	blood:	n/a
43	chr2:100824103-100824153	NHBE	bronchial:	n/a
44	chr2:100824103-100824153	HPAEpiC	pulmonary alveolar:	n/a
45	chr2:100824103-100824153	PANC-1	pancreas:	n/a
46	chr2:100824103-100824153	GM12891	blood:	n/a
47	chr2:100824103-100824153	SKMC	muscle:	n/a
48	chr2:100824103-100824153	HRCEpiC	kidney:	n/a
49	chr2:100824103-100824153	HCM	heart:	n/a
50	chr2:100824103-100824153	GM19239	blood:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:100815576..100818856-chr2:100821193..100824175,3	MCF-7	breast:

Variant related genes	Relation type
LINC01104	TF binding region
LINC01104	CpG island

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10194635	0.84[ASN][1000 genomes]
rs10496345	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10496346	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10865035	0.87[ASN][1000 genomes]
rs11123817	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11123818	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11123823	1.00[YRI][hapmap]
rs1122231	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1160542	0.84[ASN][1000 genomes]
rs1160543	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1160544	0.84[ASN][1000 genomes]
rs1160545	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11678979	0.86[ASN][1000 genomes]
rs11684761	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685491	0.88[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs11686372	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11687241	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689199	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11689201	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11690335	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691409	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691869	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11693324	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694723	1.00[YRI][hapmap]
rs11695383	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11695996	0.88[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12053126	0.82[EUR][1000 genomes]
rs12614880	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12615145	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12619178	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12712073	0.83[ASN][1000 genomes]
rs12987662	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12990462	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12991254	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12992090	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12994592	0.88[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs13002946	0.84[ASN][1000 genomes]
rs13010010	0.82[EUR][1000 genomes]
rs13013169	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13017207	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13018640	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13019179	1.00[YRI][hapmap]
rs13026143	0.82[EUR][1000 genomes]
rs13026283	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13034176	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1465800	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1465801	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2309757	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2309812	0.82[EUR][1000 genomes]
rs2309837	0.84[ASN][1000 genomes]
rs2309838	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2871344	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4303732	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4583487	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4622752	1.00[YRI][hapmap]
rs4851264	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4851266	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851268	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851269	0.85[ASN][1000 genomes]
rs4851270	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851271	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6709656	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6722241	0.82[ASN][1000 genomes]
rs6722661	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6750097	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6750505	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6754937	0.85[ASN][1000 genomes]
rs7566527	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs893246	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9653442	0.85[ASN][1000 genomes]
rs999052	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv834311	chr2:100816917-100990036	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100818600-100825000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:100820200-100825400	Enhancers	Fetal Brain Male	brain
3	chr2:100822000-100825000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:100822000-100826400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr2:100822200-100826400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr2:100822200-100830200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:100822200-100830400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:100822400-100830200	Weak transcription	Lung	lung
9	chr2:100822800-100825200	Enhancers	Fetal Lung	lung
10	chr2:100823400-100825200	Enhancers	Fetal Brain Female	brain
11	chr2:100823600-100824200	Enhancers	Fetal Heart	heart
12	chr2:100823800-100824200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:100823800-100824200	Enhancers	Placenta	Placenta
14	chr2:100823800-100824200	Bivalent Enhancer	Fetal Stomach	stomach
15	chr2:100823800-100824200	Enhancers	Left Ventricle	heart
16	chr2:100823800-100824200	Enhancers	Right Ventricle	heart
17	chr2:100823800-100824400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:100823800-100824400	Enhancers	Right Atrium	heart
19	chr2:100823800-100824600	Enhancers	Fetal Muscle Leg	muscle
20	chr2:100823800-100825200	Enhancers	Ovary	ovary
21	chr2:100824000-100824200	Enhancers	Fetal Kidney	kidney

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