Variant report

Variant	rs12028809
Chromosome Location	chr1:185140662-185140663
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:185124700..185128224-chr1:185139265..185140988,3	K562	blood:
2	chr1:185124896..185128464-chr1:185139300..185142346,3	MCF-7	breast:
3	chr1:185124480..185126123-chr1:185139685..185141251,2	MCF-7	breast:
4	chr1:185122329..185126145-chr1:185137203..185141899,4	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF2-2	chr1:185139240-185141668	NONHSAT008410
2	lnc-TRMT1L-2	chr1:185140467-185140842	NONHSAT008411

No data

Variant related genes	Relation type
ENSG00000116668	Chromatin interaction
ENSG00000121486	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1008502	1.00[CEU][hapmap]
rs1046592	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs10489581	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs10797997	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs10797998	1.00[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs10911682	0.86[EUR][1000 genomes]
rs10911686	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12022419	1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs12023744	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12025995	0.90[EUR][1000 genomes]
rs12026000	0.90[EUR][1000 genomes]
rs12030778	0.90[EUR][1000 genomes]
rs12030967	0.83[EUR][1000 genomes]
rs12031837	0.90[EUR][1000 genomes]
rs12035073	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs12035433	0.90[EUR][1000 genomes]
rs12037466	0.84[EUR][1000 genomes]
rs12037692	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs12039541	0.84[EUR][1000 genomes]
rs12040650	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs12041374	0.90[EUR][1000 genomes]
rs12043427	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs12043495	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs12043561	0.90[EUR][1000 genomes]
rs12043617	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap]
rs12044161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12044997	0.83[EUR][1000 genomes]
rs12045772	0.83[EUR][1000 genomes]
rs12046095	0.90[EUR][1000 genomes]
rs12046202	0.83[EUR][1000 genomes]
rs12086086	1.00[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs12094983	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs12401293	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12404644	1.00[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs12408279	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap]
rs12408500	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12409926	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap]
rs1407554	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1544052	1.00[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs16865296	0.83[EUR][1000 genomes]
rs2273881	0.95[EUR][1000 genomes]
rs3766719	1.00[GIH][hapmap]
rs3766720	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs3766723	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap]
rs3806243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41264588	0.86[EUR][1000 genomes]
rs41264590	0.90[EUR][1000 genomes]
rs56107433	0.90[EUR][1000 genomes]
rs61125463	0.90[EUR][1000 genomes]
rs61495015	0.90[EUR][1000 genomes]
rs72724103	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72724108	0.95[EUR][1000 genomes]
rs72741807	0.90[EUR][1000 genomes]
rs72741808	0.90[EUR][1000 genomes]
rs72741816	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72741817	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72741819	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[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	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv548396	chr1:185038104-185151378	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv521613	chr1:185071831-185171869	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185127200-185147000	Weak transcription	Spleen	Spleen
2	chr1:185127200-185169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:185127400-185144400	Weak transcription	Pancreas	Pancrea
4	chr1:185127400-185152200	Weak transcription	Aorta	Aorta
5	chr1:185127400-185153000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:185127400-185157400	Weak transcription	Small Intestine	intestine
7	chr1:185127400-185163400	Weak transcription	Esophagus	oesophagus
8	chr1:185127400-185192000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:185127600-185144400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:185127600-185144800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:185127600-185145200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:185127600-185145400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:185127600-185147400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:185127600-185170000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:185127600-185184600	Weak transcription	Psoas Muscle	Psoas
16	chr1:185127600-185218200	Weak transcription	Right Ventricle	heart
17	chr1:185127800-185147000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:185128000-185166400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:185128200-185147200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:185128200-185153800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:185128200-185161200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:185128400-185145400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:185128400-185155200	Weak transcription	NHDF-Ad	bronchial
24	chr1:185128400-185193800	Weak transcription	Brain Angular Gyrus	brain
25	chr1:185128400-185201800	Weak transcription	Gastric	stomach
26	chr1:185128600-185168200	Weak transcription	Fetal Heart	heart
27	chr1:185128600-185171400	Weak transcription	Fetal Brain Male	brain
28	chr1:185131600-185173000	Weak transcription	Brain Substantia Nigra	brain
29	chr1:185132000-185155800	Weak transcription	HSMMtube	muscle
30	chr1:185134000-185170600	Weak transcription	Lung	lung
31	chr1:185134600-185193200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:185134800-185159800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:185135000-185162800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:185135400-185141400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:185135800-185147200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:185136400-185140800	Weak transcription	Fetal Intestine Small	intestine
37	chr1:185136400-185142600	Weak transcription	Fetal Stomach	stomach
38	chr1:185136600-185167200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:185136800-185171200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr1:185137000-185143400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:185137200-185143200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:185137200-185147800	Weak transcription	Primary T cells from cord blood	blood
43	chr1:185137200-185166800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:185137200-185177200	Weak transcription	Primary B cells from cord blood	blood
45	chr1:185137200-185191400	Weak transcription	Brain Anterior Caudate	brain
46	chr1:185137400-185144400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr1:185137400-185147200	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:185137400-185152200	Weak transcription	Ovary	ovary
49	chr1:185137400-185154600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:185137400-185160000	Weak transcription	Rectal Mucosa Donor 29	rectum

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