Variant report

Variant	rs4683639
Chromosome Location	chr3:141599505-141599506
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141462888..141465330-chr3:141599094..141600858,2	K562	blood:
2	chr3:141598824..141601201-chr3:141604950..141607021,4	MCF-7	breast:
3	chr3:141599371..141601007-chr3:141713848..141716781,2	K562	blood:
4	chr3:141457377..141459578-chr3:141597906..141599752,2	MCF-7	breast:
5	chr3:141456610..141459064-chr3:141599182..141601879,3	MCF-7	breast:
6	chr3:141471164..141473196-chr3:141598108..141600224,2	K562	blood:

Variant related genes	Relation type
ENSG00000114125	Chromatin interaction
ENSG00000114126	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10755098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935439	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935440	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935441	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935443	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935446	0.86[CHB][hapmap]
rs11539489	0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11706195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707427	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710245	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11711748	0.88[CHB][hapmap]
rs11713023	0.88[CHB][hapmap]
rs11721024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11844	0.84[ASN][1000 genomes]
rs12486398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487977	0.82[ASN][1000 genomes]
rs12487983	0.84[ASN][1000 genomes]
rs12490893	0.84[ASN][1000 genomes]
rs12494971	0.88[CHB][hapmap]
rs12497443	0.88[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs1560411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16851892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288634	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs2288635	0.86[ASN][1000 genomes]
rs2288636	0.88[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs2861382	0.99[ASN][1000 genomes]
rs34071952	0.82[ASN][1000 genomes]
rs36038301	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792410	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3804772	0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs3804773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3828398	0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4683638	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683640	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683643	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683644	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683646	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683647	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4683649	0.84[ASN][1000 genomes]
rs4683651	0.80[ASN][1000 genomes]
rs55945175	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59122181	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616903	0.97[EUR][1000 genomes];1.00[ASN][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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3333253	chr3:141585303-141602936	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4683639	TFDP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141594400-141600400	Active TSS	GM12878-XiMat	blood
2	chr3:141596400-141609400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:141596400-141626400	Weak transcription	Pancreas	Pancrea
4	chr3:141597000-141600400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:141597000-141604600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:141597000-141613200	Weak transcription	Placenta	Placenta
7	chr3:141597000-141615800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:141597000-141625200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:141597000-141646400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:141597200-141600200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:141597200-141600200	Weak transcription	Primary T cells from cord blood	blood
12	chr3:141597200-141625800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:141597400-141618800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr3:141597400-141618800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:141597600-141599600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:141597800-141600200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:141597800-141600400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr3:141597800-141600400	Weak transcription	Adipose Nuclei	Adipose
19	chr3:141597800-141601400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:141597800-141601600	Weak transcription	Fetal Stomach	stomach
21	chr3:141597800-141604200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:141597800-141606000	Weak transcription	Aorta	Aorta
23	chr3:141597800-141615800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:141597800-141617200	Weak transcription	Primary B cells from cord blood	blood
25	chr3:141597800-141617400	Weak transcription	HSMM	muscle
26	chr3:141597800-141619000	Weak transcription	Lung	lung
27	chr3:141597800-141627000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr3:141598000-141600200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:141598000-141600200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:141598000-141600200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:141598000-141600200	Weak transcription	Brain Germinal Matrix	brain
32	chr3:141598000-141600200	Weak transcription	Thymus	Thymus
33	chr3:141598000-141600400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:141598000-141600400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:141598000-141601600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:141598000-141605600	Weak transcription	HSMMtube	muscle
37	chr3:141598000-141613800	Weak transcription	Fetal Lung	lung
38	chr3:141598000-141615800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:141598000-141618600	Weak transcription	Fetal Intestine Large	intestine
40	chr3:141598000-141618800	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:141598000-141619200	Weak transcription	Psoas Muscle	Psoas
42	chr3:141598000-141625400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:141598000-141626000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:141598000-141627000	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:141598000-141627200	Weak transcription	Colonic Mucosa	Colon
46	chr3:141598000-141642000	Weak transcription	Right Ventricle	heart
47	chr3:141598200-141600200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:141598200-141600200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr3:141598200-141600200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:141598200-141600200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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