Variant report

Variant	rs3769693
Chromosome Location	chr2:99259346-99259347
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99254348..99256553-chr2:99259322..99261027,2	MCF-7	breast:
2	chr2:99256152..99259010-chr2:99259230..99262017,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11887056	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12618769	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12623494	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13416843	0.94[EUR][1000 genomes]
rs17513621	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17513782	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769694	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769695	0.92[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3769696	0.92[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3769697	0.85[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55934348	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741558	0.92[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72825704	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72825708	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825710	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72825711	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72825718	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72825719	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825720	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825725	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825727	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72825732	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825733	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560357	0.85[ASW][hapmap];0.92[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013941	chr2:99116255-99317933	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv535834	chr2:99116255-99317933	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv582516	chr2:99254031-99304794	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99231200-99286200	Weak transcription	Stomach Mucosa	stomach
2	chr2:99234600-99310600	Weak transcription	Small Intestine	intestine
3	chr2:99234800-99264600	Weak transcription	Ovary	ovary
4	chr2:99234800-99296400	Weak transcription	Esophagus	oesophagus
5	chr2:99235400-99273600	Weak transcription	Fetal Kidney	kidney
6	chr2:99243600-99265800	Strong transcription	Duodenum Mucosa	Duodenum
7	chr2:99244200-99265600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr2:99244800-99265400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:99245000-99268000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:99247200-99265600	Strong transcription	HepG2	liver
11	chr2:99249800-99261600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr2:99249800-99265600	Weak transcription	Brain Substantia Nigra	brain
13	chr2:99249800-99318000	Weak transcription	Psoas Muscle	Psoas
14	chr2:99251200-99260000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:99251200-99263600	Weak transcription	Placenta	Placenta
16	chr2:99251400-99269000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:99251400-99277800	Weak transcription	Spleen	Spleen
18	chr2:99251400-99295600	Weak transcription	Fetal Stomach	stomach
19	chr2:99251600-99260200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:99251600-99260200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:99251600-99260400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:99251600-99260600	Weak transcription	Right Ventricle	heart
23	chr2:99251600-99264200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:99251600-99264200	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:99251600-99275400	Weak transcription	Gastric	stomach
26	chr2:99251600-99302000	Weak transcription	Brain Angular Gyrus	brain
27	chr2:99251600-99306600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:99251800-99275600	Weak transcription	Aorta	Aorta
29	chr2:99252200-99271200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:99253200-99277400	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:99253200-99293000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:99253600-99265000	Weak transcription	Brain Anterior Caudate	brain
33	chr2:99254400-99264000	Weak transcription	Thymus	Thymus
34	chr2:99254600-99261400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:99254600-99264000	Weak transcription	Pancreas	Pancrea
36	chr2:99254600-99265600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:99254600-99265800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:99255000-99261200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr2:99255200-99260000	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:99255200-99262400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:99255200-99265800	Strong transcription	Dnd41	blood
42	chr2:99255600-99261800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr2:99255600-99264200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr2:99255600-99265000	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr2:99255600-99265000	Strong transcription	Fetal Thymus	thymus
46	chr2:99255600-99265400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr2:99255600-99265800	Strong transcription	Fetal Intestine Large	intestine
48	chr2:99255600-99306800	Weak transcription	Colonic Mucosa	Colon
49	chr2:99255800-99264800	Strong transcription	Primary T cells from cord blood	blood
50	chr2:99255800-99265000	Strong transcription	Primary T cells fromperipheralblood	blood

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