Variant report

Variant	rs13398912
Chromosome Location	chr2:234402628-234402629
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234400105..234405009-chr2:234616033..234619892,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224814	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10171805	1.00[AMR][1000 genomes]
rs10182818	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13389374	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13390054	1.00[EUR][1000 genomes]
rs13395852	1.00[EUR][1000 genomes]
rs13401703	1.00[EUR][1000 genomes]
rs13403667	1.00[EUR][1000 genomes]
rs13406202	1.00[EUR][1000 genomes]
rs28538197	1.00[AMR][1000 genomes]
rs28898571	1.00[EUR][1000 genomes]
rs28898573	1.00[EUR][1000 genomes]
rs28968515	1.00[EUR][1000 genomes]
rs28969703	1.00[EUR][1000 genomes]
rs28969712	1.00[EUR][1000 genomes]
rs28969974	1.00[EUR][1000 genomes]
rs28970005	1.00[EUR][1000 genomes]
rs28970006	1.00[EUR][1000 genomes]
rs28970014	1.00[EUR][1000 genomes]
rs28970015	1.00[EUR][1000 genomes]
rs45498701	1.00[EUR][1000 genomes]
rs45548336	1.00[EUR][1000 genomes]
rs45568235	1.00[EUR][1000 genomes]
rs56094972	1.00[AMR][1000 genomes]
rs58587369	0.95[AFR][1000 genomes]
rs73121108	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123128	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123133	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123137	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123148	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123150	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7594222	1.00[EUR][1000 genomes]
rs9287602	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv3214	chr2:234384436-234416949	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234364000-234411200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:234373000-234409800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:234373800-234404400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:234375400-234411200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:234384000-234412400	Weak transcription	Fetal Heart	heart
6	chr2:234384600-234408400	Strong transcription	Duodenum Mucosa	Duodenum
7	chr2:234386800-234407800	Strong transcription	Fetal Intestine Large	intestine
8	chr2:234387400-234402800	Strong transcription	Adipose Nuclei	Adipose
9	chr2:234387400-234466000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:234390200-234402800	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr2:234390800-234441000	Weak transcription	Fetal Brain Male	brain
12	chr2:234391200-234404400	Strong transcription	Fetal Stomach	stomach
13	chr2:234391600-234412000	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:234392000-234411600	Weak transcription	Fetal Brain Female	brain
15	chr2:234392400-234403000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:234392800-234406400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:234393800-234403200	Strong transcription	Primary T cells from cord blood	blood
18	chr2:234394000-234403200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:234395200-234406000	Weak transcription	Fetal Kidney	kidney
20	chr2:234395400-234404200	Weak transcription	Stomach Mucosa	stomach
21	chr2:234395600-234404800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr2:234395600-234431800	Weak transcription	Colonic Mucosa	Colon
23	chr2:234395800-234408000	Strong transcription	Fetal Muscle Leg	muscle
24	chr2:234395800-234411400	Strong transcription	Liver	Liver
25	chr2:234396000-234407000	Strong transcription	HepG2	liver
26	chr2:234396400-234407600	Strong transcription	Stomach Smooth Muscle	stomach
27	chr2:234396600-234406000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:234396800-234409600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:234397800-234411400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:234398000-234406000	Weak transcription	Primary B cells from cord blood	blood
31	chr2:234398000-234452800	Weak transcription	HUVEC	blood vessel
32	chr2:234398200-234405800	Weak transcription	Brain Germinal Matrix	brain
33	chr2:234398200-234411200	Weak transcription	Esophagus	oesophagus
34	chr2:234398200-234411200	Weak transcription	Thymus	Thymus
35	chr2:234398400-234442400	Weak transcription	Hela-S3	cervix
36	chr2:234398600-234406600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:234398600-234408800	Weak transcription	NH-A	brain
38	chr2:234398600-234431800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:234398800-234407600	Strong transcription	HSMM	muscle
40	chr2:234398800-234408800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:234399000-234403200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:234399000-234404600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:234399000-234406200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr2:234399000-234408400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:234399000-234408400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:234399000-234409000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:234399000-234409200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:234399200-234402800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:234399200-234403600	Strong transcription	Brain Hippocampus Middle	brain
50	chr2:234399200-234405200	Strong transcription	Primary T helper cells PMA-I stimulated	--

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