Variant report

Variant	rs3769697
Chromosome Location	chr2:99242580-99242581
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99223676..99231123-chr2:99236273..99243561,12	MCF-7	breast:
2	chr2:99235707..99237524-chr2:99240900..99242893,3	K562	blood:
3	chr2:99231882..99233619-chr2:99241620..99243262,2	MCF-7	breast:
4	chr2:99236596..99238739-chr2:99240851..99242868,2	MCF-7	breast:
5	chr2:99235707..99237524-chr2:99241391..99242893,2	K562	blood:
6	chr2:99241190..99242773-chr2:99244709..99247701,2	MCF-7	breast:
7	chr2:99223844..99228722-chr2:99241465..99246103,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183513	Chromatin interaction
ENSG00000115446	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11887056	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11896729	0.83[YRI][hapmap]
rs12618524	0.80[YRI][hapmap]
rs12618769	0.86[ASW][hapmap];0.93[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12623494	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416843	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17034171	0.91[YRI][hapmap]
rs17513468	0.81[AFR][1000 genomes]
rs17513621	0.93[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17513782	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3754872	0.83[YRI][hapmap]
rs3769693	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]
rs3769694	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3769695	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769696	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769698	0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs3769701	0.91[YRI][hapmap]
rs3769708	0.91[YRI][hapmap]
rs4851145	0.83[YRI][hapmap]
rs4851146	0.91[YRI][hapmap]
rs55934348	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6741558	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825704	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825708	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72825710	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825718	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825719	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72825720	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72825725	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72825727	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825732	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72825733	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7560357	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[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	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

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99227200-99257400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr2:99227600-99243200	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr2:99228200-99244600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:99230200-99250600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:99231200-99247600	Weak transcription	Brain Angular Gyrus	brain
6	chr2:99231200-99286200	Weak transcription	Stomach Mucosa	stomach
7	chr2:99232400-99249000	Weak transcription	Psoas Muscle	Psoas
8	chr2:99232400-99250600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:99232600-99249400	Weak transcription	Aorta	Aorta
10	chr2:99232800-99250000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:99233400-99247200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:99233800-99247600	Weak transcription	Spleen	Spleen
13	chr2:99234000-99252800	Weak transcription	Brain Germinal Matrix	brain
14	chr2:99234200-99247600	Weak transcription	Fetal Stomach	stomach
15	chr2:99234400-99247400	Weak transcription	Right Ventricle	heart
16	chr2:99234400-99251000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:99234600-99310600	Weak transcription	Small Intestine	intestine
18	chr2:99234800-99248400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:99234800-99250800	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:99234800-99264600	Weak transcription	Ovary	ovary
21	chr2:99234800-99296400	Weak transcription	Esophagus	oesophagus
22	chr2:99235000-99247200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr2:99235400-99244200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:99235400-99248800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:99235400-99273600	Weak transcription	Fetal Kidney	kidney
26	chr2:99235600-99246600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:99235800-99245200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:99236000-99243800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:99236000-99248800	Weak transcription	Liver	Liver
30	chr2:99236000-99251200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr2:99238000-99245600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:99238000-99247400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:99238200-99246600	Weak transcription	Adipose Nuclei	Adipose
34	chr2:99238200-99247600	Weak transcription	Left Ventricle	heart
35	chr2:99238200-99247600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:99238400-99251200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:99238600-99246800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:99238600-99247200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:99238600-99247200	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:99238600-99256000	Weak transcription	Primary B cells from cord blood	blood
41	chr2:99238800-99249000	Weak transcription	Brain Substantia Nigra	brain
42	chr2:99239000-99248000	Weak transcription	Placenta	Placenta
43	chr2:99239000-99249000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:99239000-99250400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:99239200-99247400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr2:99239200-99247600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:99239400-99246200	Weak transcription	Pancreas	Pancrea
48	chr2:99239400-99246600	Weak transcription	Brain Anterior Caudate	brain
49	chr2:99239400-99246800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:99239400-99248800	Weak transcription	Colon Smooth Muscle	Colon

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