Variant report

Variant	rs6789950
Chromosome Location	chr3:142731791-142731792
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142728900..142732150-chr3:142733667..142735760,5	K562	blood:
2	chr3:142718594..142721364-chr3:142729652..142733132,4	MCF-7	breast:
3	chr3:142731640..142734706-chr3:142736602..142739585,4	K562	blood:

Variant related genes	Relation type
ENSG00000163714	Chromatin interaction
ENSG00000268129	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10935477	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16852921	0.89[CHB][hapmap]
rs1979836	0.89[CHB][hapmap]
rs28463805	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755739	0.83[CHB][hapmap]
rs3886152	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683441	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs4683719	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683720	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683725	0.86[ASN][1000 genomes]
rs6440128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73157683	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs750869	0.89[CHB][hapmap]
rs750870	0.89[CHB][hapmap]
rs7640077	0.83[CHB][hapmap]

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	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv877563	chr3:142661350-142743889	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142721400-142735800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:142721600-142739400	Weak transcription	Lung	lung
3	chr3:142721800-142734800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:142721800-142736400	Weak transcription	Ovary	ovary
5	chr3:142721800-142739200	Weak transcription	Colonic Mucosa	Colon
6	chr3:142721800-142761800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:142722000-142733000	Weak transcription	Brain Anterior Caudate	brain
8	chr3:142722000-142735800	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:142722000-142735800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:142722000-142737000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:142722000-142739000	Weak transcription	Right Ventricle	heart
12	chr3:142722000-142742400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:142722200-142735800	Weak transcription	Brain Germinal Matrix	brain
14	chr3:142722200-142735800	Weak transcription	Fetal Brain Female	brain
15	chr3:142722200-142736400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:142722200-142737000	Weak transcription	Fetal Heart	heart
17	chr3:142722200-142739000	Weak transcription	Brain Angular Gyrus	brain
18	chr3:142722200-142743000	Weak transcription	Brain Substantia Nigra	brain
19	chr3:142722400-142732800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:142722400-142733200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:142722400-142734600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:142722400-142735200	Weak transcription	Fetal Lung	lung
23	chr3:142722400-142735800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:142723000-142735200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:142723200-142736000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:142723600-142739000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:142723800-142733600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:142723800-142735600	Weak transcription	NHLF	lung
29	chr3:142723800-142736400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:142724200-142736400	Weak transcription	Small Intestine	intestine
31	chr3:142724200-142736800	Weak transcription	Fetal Brain Male	brain
32	chr3:142725000-142735200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:142725000-142735800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:142725400-142737000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:142725800-142739000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:142726600-142736400	Weak transcription	Psoas Muscle	Psoas
37	chr3:142727000-142735200	Weak transcription	Thymus	Thymus
38	chr3:142727200-142736600	Weak transcription	HepG2	liver
39	chr3:142727400-142764400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:142727800-142735600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr3:142728000-142734800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:142728000-142742400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr3:142728400-142737400	Weak transcription	Left Ventricle	heart
44	chr3:142728400-142748400	Weak transcription	Spleen	Spleen
45	chr3:142728600-142737200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:142728600-142769000	Weak transcription	Pancreas	Pancrea
47	chr3:142729200-142735200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:142729200-142758600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr3:142729200-142765000	Strong transcription	Dnd41	blood
50	chr3:142729200-142785200	Weak transcription	Aorta	Aorta

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