Variant report

Variant	rs68071013
Chromosome Location	chr3:42659954-42659955
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	chr3:42659948-42660016	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42588038..42590456-chr3:42657625..42660579,3	K562	blood:
2	chr3:42659807..42662376-chr3:42694804..42697042,2	MCF-7	breast:
3	chr3:42659157..42660714-chr3:42671631..42673408,2	K562	blood:

Variant related genes	Relation type
NKTR	TF binding region
ENSG00000230084	Chromatin interaction
ENSG00000114853	Chromatin interaction
ENSG00000114857	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1062051	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067987	0.81[EUR][1000 genomes]
rs13072295	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13085695	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13089845	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13090902	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13093680	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13095447	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17074662	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074664	0.97[ASN][1000 genomes]
rs17074669	0.97[ASN][1000 genomes]
rs17074673	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17074674	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17074680	0.97[ASN][1000 genomes]
rs17074693	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284303	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2284304	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2300057	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2300058	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2302352	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33969824	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33984028	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34683820	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34687113	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34762478	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34801786	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34852409	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34977988	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35216140	0.82[EUR][1000 genomes]
rs35506005	0.89[ASN][1000 genomes]
rs35676838	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35770315	0.97[ASN][1000 genomes]
rs35871059	0.82[EUR][1000 genomes]
rs35890296	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36033201	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36043081	0.82[EUR][1000 genomes]
rs3774401	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774402	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774404	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774406	0.89[ASN][1000 genomes]
rs3774407	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3821836	0.84[ASN][1000 genomes]
rs3846058	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846059	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3856737	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3886782	0.89[ASN][1000 genomes]
rs3900780	0.81[EUR][1000 genomes]
rs56047094	0.82[EUR][1000 genomes]
rs56797870	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57259216	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58868911	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59914338	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60232916	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60348477	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60535002	0.82[EUR][1000 genomes]
rs61149998	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441928	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66786953	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67059259	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67165547	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67533173	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67583158	0.82[EUR][1000 genomes]
rs6771105	0.82[EUR][1000 genomes]
rs6772312	0.87[ASN][1000 genomes]
rs6778982	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6782164	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67832425	0.82[EUR][1000 genomes]
rs6788548	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6790204	0.81[EUR][1000 genomes]
rs6793186	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6795296	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6797491	0.82[EUR][1000 genomes]
rs68004576	0.82[EUR][1000 genomes]
rs68028490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72864072	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73829255	0.82[EUR][1000 genomes]
rs7617403	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617736	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623867	0.81[EUR][1000 genomes]
rs7624628	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[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	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv876730	chr3:42643935-42667936	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42643200-42672800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:42643600-42675000	Weak transcription	Aorta	Aorta
3	chr3:42643800-42671200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:42644000-42660000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:42644000-42671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:42644000-42671200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:42644000-42671400	Weak transcription	HSMMtube	muscle
8	chr3:42644000-42672000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:42644200-42663200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:42644200-42672400	Weak transcription	Fetal Kidney	kidney
11	chr3:42644800-42660000	Weak transcription	Colonic Mucosa	Colon
12	chr3:42644800-42660200	Weak transcription	NH-A	brain
13	chr3:42645200-42660200	Weak transcription	HMEC	breast
14	chr3:42646000-42672000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:42647000-42671400	Weak transcription	NHEK	skin
16	chr3:42647200-42668600	Weak transcription	Brain Germinal Matrix	brain
17	chr3:42647200-42688200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr3:42647400-42672000	Weak transcription	NHLF	lung
19	chr3:42647600-42672000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:42647600-42677600	Weak transcription	Gastric	stomach
21	chr3:42648800-42672600	Weak transcription	Fetal Brain Female	brain
22	chr3:42649800-42671200	Weak transcription	Fetal Brain Male	brain
23	chr3:42650200-42660000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr3:42650400-42660000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:42650400-42660000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:42650400-42660200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:42650400-42660600	Weak transcription	Fetal Heart	heart
28	chr3:42650400-42671400	Weak transcription	Thymus	Thymus
29	chr3:42650400-42671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:42650400-42672000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:42650600-42660000	Weak transcription	Fetal Lung	lung
32	chr3:42650600-42660400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:42650600-42669400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:42650600-42669400	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:42650600-42672600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:42650600-42673000	Weak transcription	Esophagus	oesophagus
37	chr3:42650800-42660200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:42650800-42663200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:42650800-42672800	Weak transcription	Ovary	ovary
40	chr3:42651000-42660200	Weak transcription	Liver	Liver
41	chr3:42651000-42660200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr3:42651200-42693000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:42651400-42660200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:42651400-42671000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr3:42651800-42680400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:42652000-42660000	Weak transcription	NHDF-Ad	bronchial
47	chr3:42653000-42660000	Weak transcription	Fetal Intestine Large	intestine
48	chr3:42653000-42660000	Weak transcription	Placenta	Placenta
49	chr3:42653000-42660200	Weak transcription	HepG2	liver
50	chr3:42653200-42660200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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