Variant report

Variant	rs6439655
Chromosome Location	chr3:136466599-136466600
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	CEBPB	chr3:136466023-136466673	A549	lung:	n/a	chr3:136466215-136466232

No.	Distal block	Cell Line	Cell type
1	chr3:136462295..136467701-chr3:136468356..136473185,8	MCF-7	breast:
2	chr3:136460640..136463485-chr3:136464653..136466977,3	K562	blood:
3	chr3:136464546..136467728-chr3:136469677..136472541,3	MCF-7	breast:
4	chr3:136275233..136277480-chr3:136465524..136468247,2	K562	blood:

Variant related genes	Relation type
ENSG00000261758	TF binding region
ENSG00000261758	Chromatin interaction
ENSG00000118007	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10935186	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap]
rs11919030	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs12486911	1.00[YRI][hapmap]
rs1280622	0.91[EUR][1000 genomes]
rs1280624	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13433980	1.00[CHB][hapmap]
rs1484250	1.00[CHB][hapmap]
rs1681817	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1729951	0.96[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17301365	1.00[CHB][hapmap]
rs2062322	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs35874192	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4038578	0.96[CEU][hapmap];0.87[AMR][1000 genomes]
rs4038587	0.89[CEU][hapmap]
rs4408829	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs4521165	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs6439649	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs6764567	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6771713	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs6782151	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs6791142	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs6799699	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs6802702	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73230077	0.86[ASN][1000 genomes]
rs73230078	0.86[ASN][1000 genomes]
rs7432375	1.00[ASW][hapmap];0.92[CEU][hapmap];0.96[MEX][hapmap]
rs7612160	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs7616204	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7618518	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs7618871	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs7644346	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs900818	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs940174	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs9825700	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9836231	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9845950	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs9881078	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1006737	chr3:136466188-136530743	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6439655	PCCB	cis	parietal	SCAN
rs6439655	PCCB	cis	cerebellum	SCAN
rs6439655	MSL2	cis	parietal	SCAN
rs6439655	SPSB4	cis	cerebellum	SCAN
rs6439655	DBR1	cis	cerebellum	SCAN
rs6439655	PCCB	cis	multi-tissue	Pritchard

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136432400-136468200	Weak transcription	Aorta	Aorta
2	chr3:136448200-136467600	Weak transcription	HSMM	muscle
3	chr3:136448200-136467800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:136448200-136467800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:136448200-136467800	Weak transcription	HSMMtube	muscle
6	chr3:136448600-136467600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:136449000-136470000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:136450400-136467800	Weak transcription	Psoas Muscle	Psoas
9	chr3:136450600-136467800	Weak transcription	Primary B cells from cord blood	blood
10	chr3:136450800-136467800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:136450800-136467800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:136450800-136467800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:136450800-136469000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:136451000-136467800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:136453600-136467800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:136453800-136467600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:136454200-136467800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:136454200-136469200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:136454200-136470000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:136454400-136467800	Weak transcription	Liver	Liver
21	chr3:136454400-136467800	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:136454400-136469200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:136454600-136467800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:136454800-136469200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:136455000-136467000	Weak transcription	Left Ventricle	heart
26	chr3:136455800-136467800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:136456000-136467800	Weak transcription	NH-A	brain
28	chr3:136456200-136467800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:136456400-136467000	Weak transcription	Lung	lung
30	chr3:136456400-136467400	Weak transcription	Right Ventricle	heart
31	chr3:136456400-136468000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:136456600-136467800	Weak transcription	Fetal Intestine Large	intestine
33	chr3:136457400-136470000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:136458400-136470000	Weak transcription	Esophagus	oesophagus
35	chr3:136459800-136467800	Weak transcription	Fetal Kidney	kidney
36	chr3:136460200-136467800	Weak transcription	NHEK	skin
37	chr3:136460400-136468000	Weak transcription	Gastric	stomach
38	chr3:136460800-136467600	Weak transcription	K562	blood
39	chr3:136460800-136467800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:136461200-136467600	Weak transcription	Hela-S3	cervix
41	chr3:136461200-136467600	Weak transcription	Osteobl	bone
42	chr3:136461200-136467800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr3:136461200-136467800	Weak transcription	A549	lung
44	chr3:136461400-136467600	Weak transcription	NHDF-Ad	bronchial
45	chr3:136462800-136467600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:136462800-136468000	Weak transcription	NHLF	lung
47	chr3:136463200-136467800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:136463200-136467800	Weak transcription	Fetal Brain Female	brain
49	chr3:136463200-136467800	Weak transcription	Fetal Intestine Small	intestine
50	chr3:136463200-136467800	Weak transcription	Fetal Muscle Leg	muscle

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