Variant report

Variant	rs12143425
Chromosome Location	chr1:176158283-176158284
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr1:176158134-176158496	K562	blood:	n/a	n/a
2	SETDB1	chr1:176158077-176158792	U2OS	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:176150222..176152761-chr1:176157686..176160252,3	K562	blood:
2	chr1:176156157..176159032-chr1:176159209..176161354,2	K562	blood:
3	chr1:176153203..176155245-chr1:176158200..176159994,2	K562	blood:
4	chr1:176156354..176160388-chr1:176161822..176166089,4	K562	blood:

No data

Variant related genes	Relation type
RFWD2	TF binding region
ENSG00000143207	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10494497	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12116561	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12121832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12124916	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12125192	0.88[CEU][hapmap]
rs12125328	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12127204	1.00[CEU][hapmap]
rs12127719	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12128099	1.00[CEU][hapmap];0.86[AFR][1000 genomes]
rs12128327	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12129466	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12129873	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12132072	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes]
rs12133310	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12133701	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12134392	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12134984	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12135045	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12137136	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12142010	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12142461	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12144612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12144692	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12144806	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12145452	0.85[CEU][hapmap]
rs12145703	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12145778	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12146072	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1330863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4400573	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56230548	0.85[AMR][1000 genomes];0.86[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	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv872565	chr1:176058782-176172795	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176110600-176164000	Weak transcription	NHLF	lung
2	chr1:176126400-176168800	Weak transcription	Small Intestine	intestine
3	chr1:176127000-176174000	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:176128000-176175200	Weak transcription	Esophagus	oesophagus
5	chr1:176137400-176173000	Weak transcription	Right Ventricle	heart
6	chr1:176140000-176168200	Weak transcription	Psoas Muscle	Psoas
7	chr1:176142800-176162200	Weak transcription	HepG2	liver
8	chr1:176143000-176165800	Weak transcription	Lung	lung
9	chr1:176144000-176172800	Weak transcription	HMEC	breast
10	chr1:176144400-176170800	Weak transcription	K562	blood
11	chr1:176144400-176173400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:176144600-176168600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:176144800-176164600	Weak transcription	NHDF-Ad	bronchial
14	chr1:176144800-176172800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:176145000-176173200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:176146000-176171400	Weak transcription	Left Ventricle	heart
17	chr1:176146000-176173000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:176147600-176161200	Weak transcription	HUVEC	blood vessel
19	chr1:176150600-176173000	Weak transcription	Hela-S3	cervix
20	chr1:176151600-176160000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:176151800-176173000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:176152000-176159200	Weak transcription	Liver	Liver
23	chr1:176152000-176168800	Weak transcription	Primary B cells from cord blood	blood
24	chr1:176152000-176168800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr1:176152000-176173000	Weak transcription	Thymus	Thymus
26	chr1:176153000-176161000	Weak transcription	Adipose Nuclei	Adipose
27	chr1:176153000-176161200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:176153000-176162400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:176153200-176165800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:176153200-176173000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr1:176153600-176161200	Weak transcription	Primary T cells from cord blood	blood
32	chr1:176153600-176169600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:176153600-176173000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:176153600-176173000	Weak transcription	HSMM	muscle
35	chr1:176153800-176166200	Weak transcription	Dnd41	blood
36	chr1:176154200-176160200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr1:176154400-176158400	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr1:176155400-176158400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:176155600-176159200	Weak transcription	Fetal Thymus	thymus
40	chr1:176155800-176158400	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr1:176156000-176158400	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr1:176156000-176158400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr1:176156000-176158400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:176156000-176172600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:176156200-176158600	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr1:176156200-176162200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:176156400-176159600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:176156800-176158400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr1:176156800-176158600	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr1:176157000-176159000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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