Variant report

Variant	rs838715
Chromosome Location	chr2:234292684-234292685
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	MAFF	chr2:234292547-234292816	HepG2	liver:	n/a	chr2:234292633-234292651
2	RUNX3	chr2:234292640-234293041	GM12878	blood:	n/a	n/a
3	CTCF	chr2:234292620-234292910	HVMF	connective:	n/a	chr2:234292857-234292866
4	CTCF	chr2:234292661-234293057	K562	blood:	n/a	chr2:234292857-234292866
5	RAD21	chr2:234292683-234292991	HepG2	liver:	n/a	chr2:234292857-234292870
6	MAFF	chr2:234292579-234292751	K562	blood:	n/a	chr2:234292633-234292651
7	CTCF	chr2:234292675-234293070	K562	blood:	n/a	chr2:234292857-234292866
8	CTCF	chr2:234292660-234292810	HRE	kidney:	n/a	n/a
9	RAD21	chr2:234292625-234293041	HepG2	liver:	n/a	chr2:234292857-234292870
10	NR2F2	chr2:234292587-234293063	K562	blood:	n/a	n/a
11	ATF1	chr2:234292621-234292896	K562	blood:	n/a	n/a
12	MAFK	chr2:234292559-234292797	HepG2	liver:	n/a	chr2:234292635-234292650
13	ZNF384	chr2:234292672-234293009	K562	blood:	n/a	n/a
14	MYC	chr2:234292684-234292957	K562	blood:	n/a	n/a
15	HCFC1	chr2:234292677-234292876	K562	blood:	n/a	n/a
16	MAFK	chr2:234292498-234293330	HepG2	liver:	n/a	chr2:234292970-234292985 chr2:234292635-234292650 chr2:234293174-234293188 chr2:234293180-234293191 chr2:234293176-234293191 chr2:234293176-234293192 chr2:234293173-234293189 chr2:234293171-234293191
17	RAD21	chr2:234292674-234292985	K562	blood:	n/a	chr2:234292857-234292870
18	GATA3	chr2:234292588-234293001	MCF-7	breast:	n/a	chr2:234292814-234292823
19	CTCF	chr2:234292580-234292730	HAc	cerebellar:	n/a	n/a
20	ARID3A	chr2:234292671-234292913	K562	blood:	n/a	n/a
21	CTCF	chr2:234292591-234293201	A549	lung:	n/a	chr2:234292857-234292866
22	MAFK	chr2:234292545-234292887	K562	blood:	n/a	chr2:234292635-234292650
23	CTCF	chr2:234292676-234293029	K562	blood:	n/a	chr2:234292857-234292866

No.	Distal block	Cell Line	Cell type
1	chr2:234179050..234180809-chr2:234289947..234292928,2	MCF-7	breast:
2	chr2:234259434..234265610-chr2:234290886..234296562,9	MCF-7	breast:
3	chr2:234292070..234294223-chr2:234599510..234601905,2	MCF-7	breast:
4	chr2:234289741..234291350-chr2:234292115..234294515,2	K562	blood:

Variant related genes	Relation type
ENSG00000201013	TF binding region
DGKD	TF binding region
ENSG00000259793	Chromatin interaction
ENSG00000243637	Chromatin interaction
ENSG00000077044	Chromatin interaction
ENSG00000167165	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1053895	0.87[MEX][hapmap]
rs2242100	0.95[MEX][hapmap]
rs2971868	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs34339006	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4663540	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs7422272	0.96[CEU][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs768811	0.83[MEX][hapmap]
rs838707	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs838710	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs838713	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs838714	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs838718	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[ASN][1000 genomes]
rs838719	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs838720	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs838722	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs838730	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs838731	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs838732	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs838733	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs838734	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs838735	0.95[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs838715	DGKD	cis	cerebellum	SCAN
rs838715	SP100	cis	parietal	SCAN
rs838715	DGKD	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234264600-234307600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:234264800-234292800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:234265000-234295000	Weak transcription	Osteobl	bone
4	chr2:234265200-234295000	Weak transcription	NH-A	brain
5	chr2:234265800-234293000	Weak transcription	HMEC	breast
6	chr2:234266000-234293000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:234266400-234294000	Weak transcription	Fetal Brain Male	brain
8	chr2:234268400-234293400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:234269200-234293400	Weak transcription	Right Atrium	heart
10	chr2:234270000-234322400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:234272800-234313200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:234274000-234295200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:234277600-234322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:234278600-234292800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:234278600-234292800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:234278600-234293000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:234278600-234293600	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:234278600-234293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:234278600-234294000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:234278600-234294000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:234278800-234293000	Weak transcription	Brain Substantia Nigra	brain
22	chr2:234279000-234293000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:234279200-234293200	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:234279200-234293400	Weak transcription	Brain Anterior Caudate	brain
25	chr2:234279200-234293600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:234279200-234294400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:234280400-234294800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:234280600-234293200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:234281800-234296600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:234282000-234292800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:234282200-234293000	Weak transcription	Gastric	stomach
32	chr2:234282200-234293400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:234282200-234293600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:234282400-234294400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:234282400-234298000	Weak transcription	Dnd41	blood
36	chr2:234284000-234293800	Weak transcription	Colonic Mucosa	Colon
37	chr2:234284600-234292800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:234284800-234292800	Weak transcription	HSMM	muscle
39	chr2:234284800-234295400	Weak transcription	Fetal Intestine Large	intestine
40	chr2:234285000-234295400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr2:234286600-234292800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:234286600-234292800	Weak transcription	Fetal Intestine Small	intestine
43	chr2:234287400-234294800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr2:234289000-234293000	Weak transcription	Brain Germinal Matrix	brain
45	chr2:234289000-234307600	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:234289200-234293000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:234289400-234292800	Enhancers	Primary B cells from cord blood	blood
48	chr2:234289400-234293200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr2:234289400-234293400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr2:234289400-234293400	Weak transcription	Rectal Mucosa Donor 29	rectum

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