Variant report

Variant	rs6436944
Chromosome Location	chr2:231376320-231376321
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr2:231376318-231376571	Hela-S3	cervix:	n/a	chr2:231376482-231376490 chr2:231376355-231376363
2	CTCF	chr2:231376280-231376430	GM12865	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SP110-8	chr2:231374985-231376452	NONHSAT077290

Variant related genes	Relation type
HMGB1P3	TF binding region

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

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1102957	0.94[EUR][1000 genomes]
rs1104327	0.95[EUR][1000 genomes]
rs13000851	0.95[EUR][1000 genomes]
rs1622980	0.85[CEU][hapmap]
rs1649876	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1649902	0.83[EUR][1000 genomes]
rs1649906	0.95[EUR][1000 genomes]
rs1649907	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1649908	0.95[EUR][1000 genomes]
rs1649909	0.92[EUR][1000 genomes]
rs1649910	0.85[EUR][1000 genomes]
rs1649921	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1649925	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1678151	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1678187	0.95[EUR][1000 genomes]
rs1678189	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1678190	0.86[EUR][1000 genomes]
rs1678199	0.96[EUR][1000 genomes]
rs1678205	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1678210	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1678211	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2195196	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2219811	0.92[CEU][hapmap]
rs2434050	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs33078	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33079	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4973324	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4973325	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62193433	0.85[ASN][1000 genomes]
rs62195461	0.95[EUR][1000 genomes]
rs6436942	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6436945	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6717269	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6724975	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6740016	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs699660	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs699661	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs836232	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs836236	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs836237	0.95[EUR][1000 genomes]
rs836238	0.95[EUR][1000 genomes]
rs836239	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs890668	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231352600-231376800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:231355200-231380400	Strong transcription	Adipose Nuclei	Adipose
3	chr2:231355600-231378600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:231355800-231381400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:231356400-231377000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:231357200-231377800	Weak transcription	Stomach Mucosa	stomach
7	chr2:231358400-231376600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:231358600-231377400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:231359600-231380400	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:231361800-231381400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr2:231362000-231376600	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr2:231362000-231376600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:231362200-231378600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:231362400-231378400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:231362400-231378600	Strong transcription	Primary T cells from cord blood	blood
16	chr2:231362600-231378600	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr2:231362600-231380600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:231362800-231376600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr2:231363000-231376600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:231363400-231377000	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:231363800-231380200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:231364200-231381000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:231364600-231385800	Weak transcription	HSMMtube	muscle
24	chr2:231364800-231377200	Weak transcription	Fetal Intestine Large	intestine
25	chr2:231365400-231377600	Weak transcription	Fetal Intestine Small	intestine
26	chr2:231365600-231377200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:231366600-231385200	Weak transcription	HMEC	breast
28	chr2:231366800-231379800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:231367000-231378600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr2:231367200-231376600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:231368400-231378000	Strong transcription	Spleen	Spleen
32	chr2:231369200-231377600	Weak transcription	Small Intestine	intestine
33	chr2:231370800-231389600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr2:231371000-231376600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:231371000-231409800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:231371200-231377600	Weak transcription	NH-A	brain
37	chr2:231371200-231384600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr2:231372000-231377600	Weak transcription	Pancreas	Pancrea
39	chr2:231372000-231384600	Weak transcription	Placenta	Placenta
40	chr2:231372400-231379200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:231372400-231386200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:231372600-231378200	Weak transcription	Gastric	stomach
43	chr2:231372600-231379200	Weak transcription	NHLF	lung
44	chr2:231373400-231376600	Strong transcription	Primary hematopoietic stem cells	blood
45	chr2:231373400-231377200	Strong transcription	Osteobl	bone
46	chr2:231373600-231376600	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr2:231373600-231377800	Strong transcription	Lung	lung
48	chr2:231373600-231378000	Strong transcription	Left Ventricle	heart
49	chr2:231373800-231376600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:231373800-231376600	Strong transcription	Skeletal Muscle Female	skeletal muscle

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