Variant report

Variant	rs838730
Chromosome Location	chr2:234314479-234314480
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234312176..234314651-chr2:234316905..234320514,3	MCF-7	breast:
2	chr2:234313157..234314685-chr2:234334796..234337300,2	K562	blood:

Variant related genes	Relation type
ENSG00000077044	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1053895	1.00[ASW][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs2054071	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242100	0.92[ASW][hapmap];0.86[CHB][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs2924815	0.84[CEU][hapmap];0.80[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2971868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762592	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4663540	0.92[CEU][hapmap];0.81[GIH][hapmap]
rs55865137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6706384	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6723558	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7422272	0.92[CEU][hapmap];0.94[GIH][hapmap]
rs768811	0.92[ASW][hapmap];0.92[MEX][hapmap]
rs838707	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs838713	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs838714	0.96[CEU][hapmap];0.91[CHB][hapmap]
rs838715	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs838718	0.86[CHD][hapmap]
rs838719	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs838722	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs838731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838732	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs838734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs838735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[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	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs838730	DGKD	cis	cerebellum	SCAN
rs838730	DGKD	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234270000-234322400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:234277600-234322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:234294600-234318800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr2:234295800-234318200	Weak transcription	K562	blood
5	chr2:234297200-234314600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:234297200-234316800	Weak transcription	Aorta	Aorta
7	chr2:234297200-234317000	Weak transcription	Placenta	Placenta
8	chr2:234297200-234317000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:234297200-234317200	Weak transcription	Pancreas	Pancrea
10	chr2:234297200-234317400	Weak transcription	Brain Angular Gyrus	brain
11	chr2:234297200-234317400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:234297200-234318600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:234297200-234319000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:234297200-234319000	Weak transcription	Fetal Kidney	kidney
15	chr2:234297200-234319400	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:234297200-234322000	Weak transcription	Hela-S3	cervix
17	chr2:234297200-234322200	Weak transcription	Brain Anterior Caudate	brain
18	chr2:234297400-234316200	Weak transcription	Fetal Lung	lung
19	chr2:234298000-234314600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr2:234298000-234317200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:234298600-234316200	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:234299200-234316000	Weak transcription	Osteobl	bone
23	chr2:234299200-234319200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:234299200-234319200	Weak transcription	NHEK	skin
25	chr2:234300000-234318200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:234301200-234319800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:234301800-234315200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:234303000-234319000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:234305400-234317200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:234305400-234319000	Weak transcription	HSMMtube	muscle
31	chr2:234305400-234319200	Weak transcription	HSMM	muscle
32	chr2:234306400-234318000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr2:234307200-234320200	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:234308200-234318600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:234308200-234318800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:234308400-234316400	Weak transcription	Ovary	ovary
37	chr2:234308400-234317000	Weak transcription	Right Atrium	heart
38	chr2:234308400-234317200	Weak transcription	Left Ventricle	heart
39	chr2:234308400-234322200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:234308600-234317000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:234308800-234328400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:234309200-234316400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:234309200-234319000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:234309400-234317000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:234309400-234317400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:234309400-234319200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:234309400-234322000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:234309600-234314600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr2:234309600-234314600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:234309600-234316000	Weak transcription	Liver	Liver

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