Variant report

Variant	rs13403169
Chromosome Location	chr2:234338521-234338522
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	NFIC	chr2:234338472-234339310	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr2:234338504-234339750	SK-N-SH	brain:	n/a	chr2:234339238-234339246 chr2:234339235-234339248
3	GATA3	chr2:234338479-234339718	SK-N-SH	brain:	n/a	chr2:234339238-234339246 chr2:234339235-234339248
4	EP300	chr2:234338516-234339298	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr2:234338517-234339309	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr2:234338433-234339371	A549	lung:	n/a	chr2:234339238-234339246 chr2:234339235-234339248
7	POLR2A	chr2:234338061-234338617	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234337631..234339943-chr2:234342706..234345543,2	K562	blood:
2	chr2:234326124..234329247-chr2:234337323..234339781,4	MCF-7	breast:
3	chr2:234333282..234336244-chr2:234336565..234338970,2	K562	blood:
4	chr2:234331362..234333513-chr2:234338098..234340435,2	MCF-7	breast:
5	chr2:234326778..234329463-chr2:234337161..234339349,2	MCF-7	breast:

Variant related genes	Relation type
DGKD	TF binding region
ENSG00000077044	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10168794	0.88[CEU][hapmap]
rs10169180	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10178357	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10181039	0.89[EUR][1000 genomes]
rs10183033	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10185923	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10193542	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs10207915	0.82[ASN][1000 genomes]
rs10803653	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10929195	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1097930	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1097931	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs11888993	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11892545	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs11895231	0.81[EUR][1000 genomes]
rs11897617	0.97[ASN][1000 genomes]
rs1220430	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12473824	1.00[CHB][hapmap]
rs12615446	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs13384932	0.88[CEU][hapmap]
rs13391864	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs13392183	0.85[EUR][1000 genomes]
rs13400471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13400563	0.82[CEU][hapmap];0.95[EUR][1000 genomes]
rs13406462	1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13406655	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13414407	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs13419277	0.89[EUR][1000 genomes]
rs13425849	0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1453321	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1470864	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1545525	0.82[JPT][hapmap]
rs1597940	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2167884	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2167885	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2305541	0.83[ASN][1000 genomes]
rs2602387	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs2602389	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2603545	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2603547	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs28444082	0.89[EUR][1000 genomes]
rs28506837	0.89[EUR][1000 genomes]
rs28588417	0.84[EUR][1000 genomes]
rs2924811	0.88[ASN][1000 genomes]
rs2971862	0.88[ASN][1000 genomes]
rs2971863	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs2971864	0.88[ASN][1000 genomes]
rs2971867	0.88[ASN][1000 genomes]
rs3762591	0.89[EUR][1000 genomes]
rs4233627	0.82[ASN][1000 genomes]
rs59458664	0.85[ASN][1000 genomes]
rs6710645	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6713866	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6745134	0.88[CEU][hapmap]
rs6753062	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6756068	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs73117507	0.89[EUR][1000 genomes]
rs7422734	0.88[CEU][hapmap]
rs7571288	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7572257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572310	0.81[ASN][1000 genomes]
rs7578898	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7599285	0.82[ASN][1000 genomes]
rs838543	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs838544	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs838545	0.82[ASN][1000 genomes]
rs838548	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs838549	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs838550	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs838551	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs838552	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs838555	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs838559	0.87[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	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
3	nsv1000870	chr2:234333083-234410768	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234322400-234371800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:234328800-234343000	Weak transcription	Liver	Liver
3	chr2:234329000-234339200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr2:234329000-234343600	Weak transcription	Fetal Brain Female	brain
5	chr2:234329000-234351600	Weak transcription	Fetal Brain Male	brain
6	chr2:234329200-234343800	Weak transcription	Brain Germinal Matrix	brain
7	chr2:234329200-234344600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:234329400-234343200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:234329400-234343400	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:234329400-234344600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:234329400-234346000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:234330800-234343200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:234331000-234344000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:234331200-234340400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:234331200-234343400	Weak transcription	Thymus	Thymus
16	chr2:234331200-234344000	Weak transcription	Dnd41	blood
17	chr2:234331200-234344600	Weak transcription	Esophagus	oesophagus
18	chr2:234331600-234344400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:234332600-234339800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr2:234333200-234343200	Weak transcription	HepG2	liver
21	chr2:234333200-234344000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:234333400-234343000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:234333400-234343000	Weak transcription	Colonic Mucosa	Colon
24	chr2:234333400-234343000	Weak transcription	Spleen	Spleen
25	chr2:234333400-234344600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:234333400-234345600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:234333600-234338600	Weak transcription	NHLF	lung
28	chr2:234333600-234339200	Enhancers	Stomach Mucosa	stomach
29	chr2:234333600-234343000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:234333600-234343200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:234333600-234343400	Weak transcription	Lung	lung
32	chr2:234333800-234343800	Weak transcription	Fetal Intestine Large	intestine
33	chr2:234334000-234343400	Weak transcription	Fetal Intestine Small	intestine
34	chr2:234334200-234339800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr2:234334200-234340200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:234334400-234339400	Enhancers	HSMM	muscle
37	chr2:234334800-234339200	Enhancers	K562	blood
38	chr2:234335000-234338600	Enhancers	Left Ventricle	heart
39	chr2:234335200-234357600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:234335400-234339800	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr2:234335400-234340000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr2:234335600-234340400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:234335600-234343200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:234335600-234343600	Strong transcription	Primary B cells from cord blood	blood
45	chr2:234335600-234344000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:234335600-234344000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr2:234335600-234344800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:234335800-234339200	Enhancers	Primary T cells fromperipheralblood	blood
49	chr2:234335800-234344200	Weak transcription	Small Intestine	intestine
50	chr2:234336000-234338600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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