Variant report

Variant	rs6807338
Chromosome Location	chr3:56649282-56649283
allele	C/T
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	POLR2A	chr3:56649188-56649638	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:56648967-56664047	K562	blood:	n/a	n/a
3	POLR2A	chr3:56649132-56649587	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
CCDC66	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs13060656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072654	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080003	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088166	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089169	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13089332	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13090343	0.89[ASN][1000 genomes]
rs13095165	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099722	0.82[CEU][hapmap]
rs17825529	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1826119	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34097767	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34171578	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34284682	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34349699	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34480364	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34720351	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34869541	1.00[ASN][1000 genomes]
rs34885435	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34911835	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34953718	1.00[ASN][1000 genomes]
rs35070694	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35286628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35418695	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35564119	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35677810	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35689307	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35728519	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35785755	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35803417	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35940731	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35995233	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36029237	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36064180	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36131262	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732506	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4060982	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4538344	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4635676	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71309961	1.00[ASN][1000 genomes]
rs71309962	1.00[ASN][1000 genomes]
rs71309963	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71309964	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71309965	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71309970	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71309972	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71309973	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71309975	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71621834	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7431634	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv820061	chr3:56648862-56650174	Strong transcription Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56603200-56650400	Weak transcription	K562	blood
2	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
3	chr3:56607800-56650200	Weak transcription	Psoas Muscle	Psoas
4	chr3:56625200-56650400	Weak transcription	NHEK	skin
5	chr3:56625200-56653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:56626400-56656200	Weak transcription	Stomach Mucosa	stomach
7	chr3:56628600-56649600	Weak transcription	HepG2	liver
8	chr3:56630000-56654400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:56634000-56651400	Weak transcription	Fetal Brain Male	brain
10	chr3:56640000-56650000	Weak transcription	HMEC	breast
11	chr3:56640400-56650800	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:56640600-56650400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:56640600-56652600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:56640800-56649400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:56640800-56649400	Weak transcription	Osteobl	bone
16	chr3:56640800-56649800	Weak transcription	Fetal Kidney	kidney
17	chr3:56640800-56650400	Weak transcription	NHLF	lung
18	chr3:56640800-56650600	Weak transcription	HSMMtube	muscle
19	chr3:56640800-56650800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:56640800-56664200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:56640800-56695400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:56642800-56713400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:56643000-56649400	Strong transcription	Primary B cells from cord blood	blood
24	chr3:56644200-56664000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:56644400-56652000	Strong transcription	Fetal Lung	lung
26	chr3:56644400-56686400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:56644600-56655800	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:56644600-56665600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:56644600-56668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:56644800-56649600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:56644800-56649600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:56644800-56655400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:56644800-56656000	Strong transcription	Fetal Muscle Leg	muscle
34	chr3:56644800-56669800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:56644800-56708200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr3:56645000-56650600	Weak transcription	A549	lung
37	chr3:56645000-56650800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr3:56645200-56651600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:56645200-56657000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr3:56645400-56653800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:56645400-56667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:56645400-56705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr3:56645600-56650600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr3:56645600-56653400	Weak transcription	Fetal Heart	heart
45	chr3:56645600-56656000	Strong transcription	Fetal Intestine Large	intestine
46	chr3:56645600-56656000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr3:56645600-56664800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:56645600-56665800	Strong transcription	Hela-S3	cervix
49	chr3:56645800-56662000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr3:56645800-56663800	Strong transcription	HSMM	muscle

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