Variant report

Variant	rs6440128
Chromosome Location	chr3:142739103-142739104
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142731640..142734706-chr3:142736602..142739585,4	K562	blood:
2	chr3:142737884..142740234-chr3:142747413..142749018,2	MCF-7	breast:
3	chr3:142737557..142741903-chr3:142742204..142751420,11	K562	blood:

Variant related genes	Relation type
ENSG00000163714	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10935477	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16852921	0.94[CEU][hapmap];0.86[CHB][hapmap]
rs1979836	0.94[CEU][hapmap];0.86[CHB][hapmap]
rs28463805	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755739	0.81[TSI][hapmap]
rs3886152	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683441	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4683442	1.00[CEU][hapmap]
rs4683719	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683720	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683725	0.86[ASN][1000 genomes]
rs4683739	0.84[CEU][hapmap]
rs6789950	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	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs750869	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap]
rs750870	0.94[CEU][hapmap];0.86[CHB][hapmap];0.88[GIH][hapmap];0.92[TSI][hapmap]
rs7640077	0.81[TSI][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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6440128	RASA2	cis	parietal	SCAN
rs6440128	TFDP2	cis	cerebellum	SCAN
rs6440128	ZBTB38	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142721600-142739400	Weak transcription	Lung	lung
2	chr3:142721800-142739200	Weak transcription	Colonic Mucosa	Colon
3	chr3:142721800-142761800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:142722000-142742400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:142722200-142743000	Weak transcription	Brain Substantia Nigra	brain
6	chr3:142727400-142764400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:142728000-142742400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:142728400-142748400	Weak transcription	Spleen	Spleen
9	chr3:142728600-142769000	Weak transcription	Pancreas	Pancrea
10	chr3:142729200-142758600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:142729200-142765000	Strong transcription	Dnd41	blood
12	chr3:142729200-142785200	Weak transcription	Aorta	Aorta
13	chr3:142729400-142740000	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:142729400-142741600	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:142729400-142764800	Strong transcription	K562	blood
16	chr3:142729800-142764800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:142729800-142765000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:142730200-142743800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:142730200-142753400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:142730200-142765000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:142730200-142765000	Strong transcription	Fetal Thymus	thymus
22	chr3:142730400-142741600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:142730400-142742000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:142730400-142754200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr3:142730600-142753800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr3:142730800-142741400	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:142730800-142758800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:142731000-142744400	Strong transcription	Primary B cells from peripheral blood	blood
29	chr3:142731000-142749400	Strong transcription	Adipose Nuclei	Adipose
30	chr3:142731000-142754000	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:142731200-142753800	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:142732600-142741600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:142732600-142754200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:142732800-142743800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:142732800-142759000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:142732800-142765000	Strong transcription	HSMM	muscle
37	chr3:142733000-142743800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr3:142733000-142755000	Weak transcription	Stomach Mucosa	stomach
39	chr3:142733200-142744200	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr3:142733200-142754200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:142733200-142764400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:142733400-142750400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:142733800-142739600	Strong transcription	Hela-S3	cervix
44	chr3:142734000-142758800	Strong transcription	Liver	Liver
45	chr3:142734400-142747800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:142734400-142759000	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr3:142734400-142785200	Weak transcription	Esophagus	oesophagus
48	chr3:142734600-142748400	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr3:142734600-142758800	Strong transcription	GM12878-XiMat	blood
50	chr3:142734800-142741800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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