Variant report

Variant	rs1016124
Chromosome Location	chr2:99350109-99350110
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	chr2:99346676..99348606-chr2:99349694..99353065,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10173832	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10174321	0.81[ASN][1000 genomes]
rs10177696	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10194177	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10199267	0.81[EUR][1000 genomes]
rs10200288	0.92[ASN][1000 genomes]
rs10210711	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10460485	0.81[EUR][1000 genomes]
rs10496332	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11123747	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11123749	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123751	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11885883	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12471383	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12477450	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12615301	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12622931	0.81[EUR][1000 genomes]
rs12993424	0.94[ASN][1000 genomes]
rs13391483	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13391794	0.81[EUR][1000 genomes]
rs13410406	0.81[EUR][1000 genomes]
rs1514916	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1517681	0.94[ASN][1000 genomes]
rs1913621	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2013983	0.94[ASN][1000 genomes]
rs28783173	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34521960	0.94[ASN][1000 genomes]
rs35477458	0.94[ASN][1000 genomes]
rs41445250	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4851150	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851153	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4851154	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58666702	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60024860	0.81[EUR][1000 genomes]
rs6733957	0.81[EUR][1000 genomes]
rs6737760	0.81[EUR][1000 genomes]
rs6740656	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7420869	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7558236	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7577636	0.81[EUR][1000 genomes]
rs7599792	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	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
2	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
3	nsv535836	chr2:99329084-99353519	Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv535837	chr2:99329084-99358356	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv535838	chr2:99335416-99358356	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99348400-99352600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:99348400-99352600	Weak transcription	Small Intestine	intestine
3	chr2:99348400-99367000	Weak transcription	Esophagus	oesophagus
4	chr2:99348600-99353000	Weak transcription	NHEK	skin
5	chr2:99348600-99359200	Weak transcription	Aorta	Aorta
6	chr2:99348800-99350800	Weak transcription	Thymus	Thymus
7	chr2:99348800-99351800	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr2:99348800-99352600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:99348800-99353000	Weak transcription	HMEC	breast
10	chr2:99348800-99360600	Weak transcription	Lung	lung
11	chr2:99349000-99350200	Enhancers	Placenta	Placenta
12	chr2:99349000-99350800	Weak transcription	GM12878-XiMat	blood
13	chr2:99349000-99351400	Weak transcription	Brain Anterior Caudate	brain
14	chr2:99349000-99351400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:99349000-99351400	Weak transcription	Stomach Mucosa	stomach
16	chr2:99349200-99350400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr2:99349200-99350600	Enhancers	Primary T cells fromperipheralblood	blood
18	chr2:99349200-99350600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:99349200-99350600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:99349200-99350600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:99349200-99350600	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr2:99349200-99350800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:99349200-99350800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr2:99349200-99350800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:99349200-99351400	Weak transcription	Psoas Muscle	Psoas
26	chr2:99349200-99357200	Enhancers	HepG2	liver
27	chr2:99349400-99350600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr2:99349400-99350600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:99349400-99350800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr2:99349400-99350800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:99349400-99350800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr2:99349400-99350800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:99349400-99351400	Weak transcription	Spleen	Spleen
34	chr2:99349400-99352600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:99349400-99353800	Weak transcription	Pancreas	Pancrea
36	chr2:99349400-99355800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:99349600-99350600	Weak transcription	Fetal Intestine Large	intestine
38	chr2:99349600-99350800	Weak transcription	Fetal Intestine Small	intestine
39	chr2:99349600-99350800	Enhancers	Dnd41	blood
40	chr2:99349600-99351000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr2:99349800-99350200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr2:99349800-99350200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr2:99349800-99350400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:99349800-99350400	Weak transcription	HUVEC	blood vessel
45	chr2:99349800-99350600	Enhancers	Primary T cells from cord blood	blood
46	chr2:99349800-99351000	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr2:99349800-99355200	Enhancers	Fetal Thymus	thymus
48	chr2:99350000-99350400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:99350000-99350600	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr2:99350000-99351400	Weak transcription	Colonic Mucosa	Colon

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