Variant report

Variant	rs56163086
Chromosome Location	chr2:99298202-99298203
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99296638..99298946-chr2:99305631..99307983,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10165386	0.89[EUR][1000 genomes]
rs10199926	0.86[EUR][1000 genomes]
rs10207287	0.84[EUR][1000 genomes]
rs17448085	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17448190	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17448211	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17448420	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17514013	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309434	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3769688	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769689	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55633363	0.85[EUR][1000 genomes]
rs55634708	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55646762	0.86[EUR][1000 genomes]
rs55730719	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55859362	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55939630	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56027617	0.85[EUR][1000 genomes]
rs56070038	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56305624	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56354279	0.86[EUR][1000 genomes]
rs56371690	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56375699	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56945529	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60889948	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62157995	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62157997	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62157999	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158000	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158001	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158002	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158008	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62158009	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62158010	0.85[EUR][1000 genomes]
rs62158012	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62158015	0.85[EUR][1000 genomes]
rs6742636	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72825754	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
4	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv2841	chr2:99296874-99342362	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99234600-99310600	Weak transcription	Small Intestine	intestine
2	chr2:99249800-99318000	Weak transcription	Psoas Muscle	Psoas
3	chr2:99251600-99302000	Weak transcription	Brain Angular Gyrus	brain
4	chr2:99251600-99306600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:99255600-99306800	Weak transcription	Colonic Mucosa	Colon
6	chr2:99264600-99299000	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:99265600-99306600	Weak transcription	Lung	lung
8	chr2:99265800-99303800	Weak transcription	Brain Substantia Nigra	brain
9	chr2:99266400-99304200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:99276000-99301400	Weak transcription	Aorta	Aorta
11	chr2:99279200-99302200	Weak transcription	Right Ventricle	heart
12	chr2:99282800-99306600	Weak transcription	Left Ventricle	heart
13	chr2:99286400-99301400	Weak transcription	Pancreas	Pancrea
14	chr2:99286800-99304800	Weak transcription	Gastric	stomach
15	chr2:99288000-99310000	Weak transcription	Thymus	Thymus
16	chr2:99291400-99299800	Weak transcription	HUVEC	blood vessel
17	chr2:99291400-99302000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:99291600-99302200	Weak transcription	Liver	Liver
19	chr2:99291600-99302200	Weak transcription	Brain Anterior Caudate	brain
20	chr2:99291600-99302200	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:99291800-99299000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:99292000-99310400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr2:99292200-99298400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr2:99292200-99306600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:99292200-99312800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr2:99293400-99325200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:99293800-99300000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:99293800-99302000	Weak transcription	HepG2	liver
29	chr2:99294000-99300200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr2:99294000-99302000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:99294000-99304200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:99294200-99300000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:99294200-99313600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:99294200-99315000	Weak transcription	Fetal Intestine Large	intestine
35	chr2:99294400-99315000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:99294400-99318600	Weak transcription	Spleen	Spleen
37	chr2:99294600-99306600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:99294600-99312600	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr2:99294600-99314200	Weak transcription	Fetal Intestine Small	intestine
40	chr2:99295000-99300800	Weak transcription	Primary T cells from cord blood	blood
41	chr2:99295000-99306000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:99295000-99325200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:99295200-99312600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr2:99295600-99299600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:99295600-99302400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:99295600-99310000	Weak transcription	Fetal Thymus	thymus
47	chr2:99295600-99310400	Weak transcription	Dnd41	blood
48	chr2:99297000-99299800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:99297200-99299000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr2:99297200-99300000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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