Variant report

Variant	rs56171035
Chromosome Location	chr3:101111108-101111109
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:101105681..101107819-chr3:101109398..101112235,3	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11707689	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708616	0.88[EUR][1000 genomes]
rs11710016	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11711808	0.87[EUR][1000 genomes]
rs12638137	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12638796	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17402964	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55710435	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57880921	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58835747	0.87[EUR][1000 genomes]
rs59359251	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6791964	0.82[EUR][1000 genomes]
rs72940399	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72942211	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72944107	0.93[EUR][1000 genomes]
rs72946021	0.83[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	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3439278	chr3:100936513-101162102	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1003475	chr3:101005238-101120030	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56171035	SENP7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101085600-101137600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:101096800-101111600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:101099000-101114600	Weak transcription	K562	blood
4	chr3:101106000-101111200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:101106000-101111400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:101106600-101114600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:101106800-101112200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:101106800-101133000	Weak transcription	Left Ventricle	heart
9	chr3:101106800-101133000	Weak transcription	Pancreas	Pancrea
10	chr3:101106800-101133000	Weak transcription	Spleen	Spleen
11	chr3:101107000-101114000	Weak transcription	Fetal Thymus	thymus
12	chr3:101107000-101118600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:101107000-101140800	Weak transcription	Esophagus	oesophagus
14	chr3:101107200-101111600	Weak transcription	Lung	lung
15	chr3:101107200-101133000	Weak transcription	Gastric	stomach
16	chr3:101107200-101133000	Weak transcription	Thymus	Thymus
17	chr3:101107200-101161200	Weak transcription	Aorta	Aorta
18	chr3:101108200-101112600	Weak transcription	Ovary	ovary
19	chr3:101108400-101111400	Weak transcription	Fetal Kidney	kidney
20	chr3:101108600-101111400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:101108600-101111400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:101108600-101112600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr3:101108600-101113600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:101108600-101114600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:101108600-101114600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr3:101108600-101116400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:101108600-101119400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:101108600-101138000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:101108800-101111400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr3:101108800-101113000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:101109400-101133600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:101109600-101111400	Weak transcription	Dnd41	blood
33	chr3:101109800-101127000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr3:101110200-101114200	ZNF genes & repeats	Primary T cells from cord blood	blood
35	chr3:101110400-101123800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:101110600-101113600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr3:101110600-101124000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:101110800-101111200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr3:101110800-101111400	Weak transcription	Primary B cells from cord blood	blood
40	chr3:101110800-101132400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr3:101111000-101111200	Weak transcription	Liver	Liver
42	chr3:101111000-101111200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr3:101111000-101115600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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