Variant report

Variant	rs838733
Chromosome Location	chr2:234323261-234323262
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	SP1	chr2:234321610-234323503	A549	lung:	n/a	n/a
2	JUND	chr2:234322144-234323385	A549	lung:	n/a	chr2:234322466-234322477 chr2:234322468-234322479 chr2:234322367-234322378
3	NR3C1	chr2:234322087-234323347	A549	lung:	n/a	chr2:234322368-234322377 chr2:234322469-234322478
4	FOSL2	chr2:234322024-234323373	A549	lung:	n/a	chr2:234322466-234322477 chr2:234322468-234322479 chr2:234322367-234322378
5	RCOR1	chr2:234321742-234323343	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr2:234323120-234323270	AG04449	skin:	n/a	chr2:234323146-234323155
7	SIX5	chr2:234321888-234324518	A549	lung:	n/a	n/a
8	JUND	chr2:234321994-234324377	HCT-116	colon:	n/a	chr2:234322466-234322477 chr2:234324011-234324021 chr2:234322468-234322479 chr2:234324012-234324020 chr2:234324012-234324020 chr2:234324013-234324020 chr2:234322367-234322378
9	MYC	chr2:234323198-234323361	MCF10A-Er-Src	breast:	n/a	n/a
10	TCF12	chr2:234322028-234323321	A549	lung:	n/a	n/a
11	POLR2A	chr2:234322930-234323318	U87	brain:	n/a	n/a
12	POLR2A	chr2:234322663-234323271	Hela-S3	cervix:	n/a	n/a
13	JUND	chr2:234321724-234323551	SK-N-SH	brain:	n/a	chr2:234322466-234322477 chr2:234322468-234322479 chr2:234322367-234322378
14	EP300	chr2:234321524-234324379	A549	lung:	n/a	chr2:234324011-234324020 chr2:234322103-234322117
15	POLR2A	chr2:234322090-234323381	U87	brain:	n/a	n/a
16	PBX3	chr2:234322004-234323461	SK-N-SH	brain:	n/a	chr2:234322771-234322791
17	SMARCC1	chr2:234321907-234323329	Hela-S3	cervix:	n/a	n/a
18	GATA3	chr2:234322043-234323477	SK-N-SH	brain:	n/a	n/a
19	NFIC	chr2:234322066-234323513	SK-N-SH	brain:	n/a	chr2:234322434-234322450 chr2:234322434-234322451
20	TCF12	chr2:234322042-234323428	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr2:234322206-234323357	U87	brain:	n/a	n/a
22	TEAD4	chr2:234321763-234323375	A549	lung:	n/a	n/a
23	FOSL1	chr2:234321964-234323470	HCT-116	colon:	n/a	chr2:234322466-234322477 chr2:234322468-234322479 chr2:234322367-234322378
24	REST	chr2:234322026-234323702	A549	lung:	n/a	n/a
25	RAD21	chr2:234322992-234323268	SK-N-SH_RA	brain:	n/a	n/a
26	PBX3	chr2:234322105-234323351	SK-N-SH	brain:	n/a	chr2:234322771-234322791
27	RAD21	chr2:234322653-234323425	A549	lung:	n/a	n/a
28	SMC3	chr2:234322160-234323323	Hela-S3	cervix:	n/a	n/a
29	FOXA2	chr2:234322118-234323335	A549	lung:	n/a	n/a
30	EP300	chr2:234322040-234323546	SK-N-SH	brain:	n/a	chr2:234322103-234322117
31	MAX	chr2:234322021-234323453	A549	lung:	n/a	chr2:234322320-234322330
32	NR3C1	chr2:234322100-234323338	A549	lung:	n/a	chr2:234322368-234322377 chr2:234322469-234322478
33	MAX	chr2:234321709-234323291	Hela-S3	cervix:	n/a	chr2:234322320-234322330
34	STAT1	chr2:234323143-234324464	Hela-S3	cervix:	n/a	chr2:234324035-234324044 chr2:234324036-234324045 chr2:234324034-234324045 chr2:234324036-234324059
35	FOSL2	chr2:234321536-234324442	A549	lung:	n/a	chr2:234322466-234322477 chr2:234324011-234324021 chr2:234322468-234322479 chr2:234324012-234324020 chr2:234324012-234324020 chr2:234324013-234324020 chr2:234322367-234322378
36	JUND	chr2:234322042-234323513	SK-N-SH	brain:	n/a	chr2:234322466-234322477 chr2:234322468-234322479 chr2:234322367-234322378
37	RXRA	chr2:234322049-234323446	SK-N-SH	brain:	n/a	chr2:234322943-234322962 chr2:234323245-234323254
38	JUND	chr2:234321736-234323301	Hela-S3	cervix:	n/a	chr2:234322466-234322477 chr2:234322468-234322479 chr2:234322367-234322378
39	BCL3	chr2:234322078-234323660	A549	lung:	n/a	chr2:234323245-234323254
40	CEBPB	chr2:234322171-234323367	A549	lung:	n/a	n/a
41	RAD21	chr2:234322324-234323354	Hela-S3	cervix:	n/a	n/a
42	TCF12	chr2:234321567-234324262	A549	lung:	n/a	chr2:234323747-234323757 chr2:234324007-234324014
43	EP300	chr2:234321968-234323432	A549	lung:	n/a	chr2:234322103-234322117
44	SP1	chr2:234321665-234323425	A549	lung:	n/a	n/a
45	MAX	chr2:234321767-234323358	A549	lung:	n/a	chr2:234322320-234322330
46	GATA3	chr2:234320854-234324466	A549	lung:	n/a	n/a
47	SIN3AK20	chr2:234322071-234323417	A549	lung:	n/a	n/a
48	TCF12	chr2:234321974-234323541	SK-N-SH	brain:	n/a	n/a
49	GATA3	chr2:234321632-234323519	SK-N-SH	brain:	n/a	n/a
50	FOSL1	chr2:234322054-234323497	HCT-116	colon:	n/a	chr2:234322466-234322477 chr2:234322468-234322479 chr2:234322367-234322378

No.	Distal block	Cell Line	Cell type
1	chr2:234322925..234327112-chr2:234328162..234331354,4	K562	blood:
2	chr2:234320676..234323507-chr2:234330970..234332948,2	MCF-7	breast:
3	chr2:234322925..234325669-chr2:234328162..234330584,2	K562	blood:

Variant related genes	Relation type
DGKD	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2242100	0.92[ASW][hapmap];0.86[CHB][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap]
rs2924815	0.84[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2971868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3762592	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4663540	0.92[CEU][hapmap]
rs55865137	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6706384	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6723558	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7422272	0.92[CEU][hapmap];0.90[GIH][hapmap]
rs768811	0.92[ASW][hapmap];0.92[MEX][hapmap]
rs838707	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs838713	0.88[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap]
rs838714	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs838715	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]
rs838718	0.86[CHD][hapmap]
rs838719	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs838722	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs838730	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]
rs838731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs838732	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs838734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs838733	DGKD	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234308800-234328400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:234312600-234327400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr2:234317000-234327400	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr2:234317200-234327400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:234317800-234327400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:234319200-234326000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr2:234319200-234326400	Weak transcription	Fetal Thymus	thymus
8	chr2:234319200-234326800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr2:234319200-234326800	Weak transcription	Thymus	Thymus
10	chr2:234321000-234327200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr2:234321000-234327200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr2:234321000-234327600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:234321200-234324400	Strong transcription	Primary B cells from cord blood	blood
14	chr2:234321400-234326800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr2:234321400-234326800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:234321400-234328000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:234321600-234323400	Enhancers	Primary T cells fromperipheralblood	blood
18	chr2:234321600-234324600	Enhancers	NHEK	skin
19	chr2:234321600-234325800	Enhancers	Stomach Mucosa	stomach
20	chr2:234321600-234328000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:234321800-234323400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:234321800-234323400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:234321800-234323400	Enhancers	Fetal Muscle Trunk	muscle
24	chr2:234321800-234323800	Enhancers	Adipose Nuclei	Adipose
25	chr2:234321800-234324200	Enhancers	Colonic Mucosa	Colon
26	chr2:234321800-234324400	Enhancers	HUVEC	blood vessel
27	chr2:234321800-234324600	Enhancers	HMEC	breast
28	chr2:234321800-234325200	Enhancers	Small Intestine	intestine
29	chr2:234322000-234323400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:234322000-234323400	Flanking Active TSS	Osteobl	bone
31	chr2:234322000-234324200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:234322000-234324200	Enhancers	Colon Smooth Muscle	Colon
33	chr2:234322000-234324200	Enhancers	NHDF-Ad	bronchial
34	chr2:234322000-234324400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:234322000-234324400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:234322000-234324400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:234322000-234324600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:234322000-234324600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:234322000-234324600	Enhancers	NH-A	brain
40	chr2:234322000-234326600	Genic enhancers	Primary B cells from peripheral blood	blood
41	chr2:234322200-234323400	Enhancers	Brain Anterior Caudate	brain
42	chr2:234322200-234323400	Enhancers	Lung	lung
43	chr2:234322200-234323600	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr2:234322200-234323600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:234322200-234323600	Genic enhancers	Duodenum Mucosa	Duodenum
46	chr2:234322200-234323600	Enhancers	Placenta	Placenta
47	chr2:234322200-234323600	Enhancers	Ovary	ovary
48	chr2:234322200-234323800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:234322200-234324000	Enhancers	Liver	Liver
50	chr2:234322200-234324200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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