Variant report

Variant	rs2029354
Chromosome Location	chr1:92181670-92181671
allele	A/C
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	RCOR1	chr1:92181619-92182405	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:92181357..92183863-chr1:92196120..92197770,2	K562	blood:
2	chr1:92160729..92163460-chr1:92181543..92183054,2	K562	blood:
3	chr1:92180489..92182487-chr1:92191711..92193965,2	K562	blood:

Variant related genes	Relation type
TGFBR3	TF binding region
ENSG00000069702	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1012069	0.82[CEU][hapmap]
rs11165347	0.87[CEU][hapmap]
rs12040094	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1542703	0.82[CEU][hapmap]
rs17131539	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17884552	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2007686	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029355	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296620	0.86[CEU][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296622	0.82[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs284877	0.82[CEU][hapmap]
rs3754014	0.87[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767569	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4658260	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4658261	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6699304	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs72714444	0.84[AMR][1000 genomes];0.90[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	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv2763581	chr1:92068967-92203803	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1014990	chr1:92084142-92206674	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92152600-92184200	Strong transcription	HepG2	liver
2	chr1:92153000-92197000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:92155800-92191200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:92159800-92183800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:92164000-92184400	Weak transcription	Hela-S3	cervix
6	chr1:92164000-92195000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:92165800-92184800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:92165800-92196800	Weak transcription	Small Intestine	intestine
9	chr1:92166600-92191000	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:92167400-92184800	Weak transcription	A549	lung
11	chr1:92168000-92191000	Weak transcription	HUVEC	blood vessel
12	chr1:92169800-92187200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:92171000-92196800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:92171200-92196800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:92172800-92197000	Weak transcription	Colonic Mucosa	Colon
16	chr1:92173200-92182400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr1:92173200-92202400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:92173600-92185000	Weak transcription	Gastric	stomach
19	chr1:92173600-92197800	Weak transcription	Brain Angular Gyrus	brain
20	chr1:92173800-92184400	Weak transcription	Fetal Intestine Small	intestine
21	chr1:92173800-92184600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:92174400-92184400	Weak transcription	Esophagus	oesophagus
23	chr1:92174400-92191200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:92174600-92184800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:92176800-92184400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:92177800-92181800	Genic enhancers	NHDF-Ad	bronchial
27	chr1:92178000-92185000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:92178200-92183600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:92178800-92184800	Weak transcription	Right Ventricle	heart
30	chr1:92179000-92184800	Weak transcription	Psoas Muscle	Psoas
31	chr1:92179000-92191600	Strong transcription	Placenta	Placenta
32	chr1:92179200-92184200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:92179200-92184800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:92179200-92187800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr1:92179200-92189800	Weak transcription	Right Atrium	heart
36	chr1:92179400-92181800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:92179400-92183600	Weak transcription	Fetal Kidney	kidney
38	chr1:92179400-92184800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:92179400-92185000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:92179400-92186800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:92179400-92189800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr1:92179400-92190200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:92179400-92191000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:92179400-92192600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:92179400-92195200	Weak transcription	GM12878-XiMat	blood
46	chr1:92179600-92184400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:92179600-92189800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:92179800-92182600	Strong transcription	Fetal Muscle Trunk	muscle
49	chr1:92180000-92189600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:92180200-92182200	Strong transcription	Colon Smooth Muscle	Colon

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