Variant report

Variant	rs6746628
Chromosome Location	chr2:53985466-53985467
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17045392	1.00[EUR][1000 genomes]
rs2009142	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs2009143	0.81[ASN][1000 genomes]
rs2302878	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs59689026	0.91[AFR][1000 genomes]
rs6747749	1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7589527	1.00[CEU][hapmap];0.82[AFR][1000 genomes];1.00[EUR][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	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv979005	chr2:53982124-53989634	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53910000-53994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:53910200-53990600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr2:53918400-53994000	Weak transcription	Fetal Heart	heart
4	chr2:53937000-53994400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:53937200-53994200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:53937400-53990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr2:53937400-53994400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:53938400-53992400	Weak transcription	K562	blood
9	chr2:53958200-53994400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:53963000-53994000	Weak transcription	A549	lung
11	chr2:53967200-53990200	Weak transcription	Gastric	stomach
12	chr2:53971200-53990200	Weak transcription	Pancreas	Pancrea
13	chr2:53973400-53994400	Weak transcription	Colonic Mucosa	Colon
14	chr2:53975600-53989200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr2:53975600-53990200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:53975800-53994400	Weak transcription	Fetal Kidney	kidney
17	chr2:53976600-53988600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:53977800-53989600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:53978200-53990200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:53978800-53994200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:53979200-53990200	Weak transcription	HUVEC	blood vessel
22	chr2:53979400-53994000	Weak transcription	Osteobl	bone
23	chr2:53979600-53987200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr2:53979600-53989400	Weak transcription	NH-A	brain
25	chr2:53979800-53990200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:53979800-53990200	Weak transcription	Esophagus	oesophagus
27	chr2:53979800-53994200	Weak transcription	Psoas Muscle	Psoas
28	chr2:53979800-53994200	Weak transcription	NHLF	lung
29	chr2:53980000-53990200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:53980600-53988600	Weak transcription	GM12878-XiMat	blood
31	chr2:53980600-53990400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:53981600-53990200	Weak transcription	Aorta	Aorta
33	chr2:53982000-53985800	Strong transcription	Fetal Thymus	thymus
34	chr2:53982000-53988600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr2:53982200-53985600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:53982400-53990200	Weak transcription	NHEK	skin
37	chr2:53982400-53990800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:53982400-53991600	Weak transcription	Stomach Mucosa	stomach
39	chr2:53982400-53991800	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr2:53982400-53994400	Weak transcription	NHDF-Ad	bronchial
41	chr2:53982800-53990200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:53982800-53994000	Weak transcription	HMEC	breast
43	chr2:53982800-53994200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:53983000-53985800	Strong transcription	Fetal Brain Female	brain
45	chr2:53983000-53987000	Strong transcription	Fetal Muscle Leg	muscle
46	chr2:53983000-53987000	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr2:53983000-53989400	Weak transcription	HSMM	muscle
48	chr2:53983000-53994000	Weak transcription	Small Intestine	intestine
49	chr2:53983200-53989000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:53983200-53989000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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