Variant report

Variant	rs12614876
Chromosome Location	chr2:38797374-38797375
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	POLR2A	chr2:38797191-38797501	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:38797210-38797404	MCF-7	breast:	n/a	n/a
3	POLR2A	chr2:38793541-38809540	K562	blood:	n/a	n/a
4	GATA3	chr2:38797296-38797405	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:38796992..38800688-chr2:38976632..38979355,3	K562	blood:

Variant related genes	Relation type
HNRNPLL	TF binding region
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12616367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12619629	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12621565	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12621788	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13398507	0.80[ASN][1000 genomes]
rs1543881	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17576044	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs17603782	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs34133986	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36024292	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3765001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55785223	1.00[EUR][1000 genomes]
rs55833813	1.00[EUR][1000 genomes]
rs56956410	1.00[EUR][1000 genomes]
rs58720388	0.83[EUR][1000 genomes]
rs59065420	0.83[EUR][1000 genomes]
rs6544165	1.00[CEU][hapmap]
rs6754893	1.00[EUR][1000 genomes]
rs6760965	1.00[CEU][hapmap]
rs72895897	1.00[EUR][1000 genomes]
rs72905831	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72905839	1.00[EUR][1000 genomes]
rs72913653	0.83[ASN][1000 genomes]
rs72913657	0.81[ASN][1000 genomes]
rs73929040	1.00[EUR][1000 genomes]
rs73929052	1.00[EUR][1000 genomes]
rs7578356	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs7579783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs7584862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs7606515	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38763600-38809600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:38768200-38812800	Weak transcription	Psoas Muscle	Psoas
3	chr2:38775800-38821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:38777000-38807200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:38779000-38818200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:38779400-38821800	Weak transcription	Right Ventricle	heart
7	chr2:38779600-38807400	Weak transcription	Fetal Heart	heart
8	chr2:38779600-38812800	Weak transcription	Aorta	Aorta
9	chr2:38779800-38800200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:38781200-38827600	Weak transcription	Esophagus	oesophagus
11	chr2:38781600-38797600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:38782400-38819000	Strong transcription	Fetal Thymus	thymus
13	chr2:38782800-38799000	Strong transcription	HSMM	muscle
14	chr2:38783600-38797600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:38783800-38827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:38785000-38827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:38785400-38801400	Weak transcription	GM12878-XiMat	blood
18	chr2:38786000-38827600	Weak transcription	Colonic Mucosa	Colon
19	chr2:38786400-38806200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:38786400-38818800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:38786600-38799000	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:38786600-38819000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:38787200-38798400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:38787200-38798800	Strong transcription	Osteobl	bone
25	chr2:38787200-38799200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr2:38787200-38800600	Strong transcription	NHDF-Ad	bronchial
27	chr2:38787200-38802800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr2:38787200-38805600	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:38787200-38806200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:38787200-38807000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:38787200-38807000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:38787400-38798000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:38787400-38799200	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:38787400-38802400	Strong transcription	HepG2	liver
35	chr2:38787400-38804400	Strong transcription	Placenta	Placenta
36	chr2:38787400-38806400	Strong transcription	Dnd41	blood
37	chr2:38787800-38798800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:38790600-38799200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:38790800-38799200	Strong transcription	NH-A	brain
40	chr2:38790800-38807000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr2:38791200-38798400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:38791200-38798600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:38791200-38799200	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr2:38791200-38800600	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:38791200-38801800	Strong transcription	Duodenum Mucosa	Duodenum
46	chr2:38791200-38802200	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr2:38791200-38805200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr2:38791400-38800600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:38791400-38801800	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr2:38791600-38800600	Strong transcription	Primary T cells fromperipheralblood	blood

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