Variant report

Variant	rs28380017
Chromosome Location	chr7:138200876-138200877
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:138144273..138147062-chr7:138199670..138202711,4	K562	blood:
2	chr7:138194787..138197500-chr7:138199534..138201806,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122779	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10216085	1.00[AMR][1000 genomes]
rs10224459	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10224559	0.89[AFR][1000 genomes]
rs10226487	0.89[AFR][1000 genomes]
rs10231698	0.89[AFR][1000 genomes]
rs10232597	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10234810	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10236859	0.89[AFR][1000 genomes]
rs10237069	0.89[AFR][1000 genomes]
rs10237544	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10237720	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10239129	0.83[AFR][1000 genomes]
rs10239202	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10239932	0.89[AFR][1000 genomes]
rs10241288	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10241942	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10242105	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10243069	0.89[AFR][1000 genomes]
rs10245088	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10248604	0.89[AFR][1000 genomes]
rs10253989	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10254440	0.89[AFR][1000 genomes]
rs10254935	0.86[AFR][1000 genomes]
rs10256094	0.89[AFR][1000 genomes]
rs10256358	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10256619	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10259673	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10267577	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10268912	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10272478	0.89[AFR][1000 genomes]
rs10277465	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10278741	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10281487	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1073255	0.89[AFR][1000 genomes]
rs13438570	0.89[AFR][1000 genomes]
rs28392567	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28407067	0.89[AFR][1000 genomes]
rs28498774	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28502705	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28534820	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28584756	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28598597	0.89[AFR][1000 genomes]
rs28608602	0.89[AFR][1000 genomes]
rs28673291	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28688534	0.89[AFR][1000 genomes]
rs28694658	0.89[AFR][1000 genomes]
rs28706910	1.00[AMR][1000 genomes]
rs28707292	0.89[AFR][1000 genomes]
rs28729263	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28762120	0.86[AFR][1000 genomes]
rs28764878	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28816768	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28822161	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2883144	1.00[AMR][1000 genomes]
rs3847123	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3847124	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4329204	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6947993	1.00[AMR][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	esv34048	chr7:137724092-138213119	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831153	chr7:138078179-138265648	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1030956	chr7:138163169-138579519	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:138175200-138201200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr7:138176600-138203600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr7:138177000-138212600	Weak transcription	Pancreas	Pancrea
4	chr7:138178600-138212200	Weak transcription	NHLF	lung
5	chr7:138180200-138204200	Weak transcription	Brain Substantia Nigra	brain
6	chr7:138183000-138203600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr7:138184800-138204000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr7:138186600-138210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr7:138187400-138203800	Weak transcription	Psoas Muscle	Psoas
10	chr7:138187600-138202600	Weak transcription	Hela-S3	cervix
11	chr7:138187600-138203600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr7:138188000-138204200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr7:138188200-138203800	Weak transcription	Colonic Mucosa	Colon
14	chr7:138188400-138201800	Weak transcription	NH-A	brain
15	chr7:138188400-138209800	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr7:138188600-138203600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr7:138188800-138210400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr7:138188800-138210600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr7:138189000-138203200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr7:138190200-138212200	Weak transcription	HMEC	breast
21	chr7:138191000-138201200	Weak transcription	Small Intestine	intestine
22	chr7:138191600-138201600	Weak transcription	Esophagus	oesophagus
23	chr7:138191600-138202000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr7:138191600-138203800	Weak transcription	HSMM	muscle
25	chr7:138192000-138201000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr7:138192000-138212200	Weak transcription	Stomach Mucosa	stomach
27	chr7:138192200-138207400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr7:138193600-138203200	Weak transcription	HUVEC	blood vessel
29	chr7:138193600-138204000	Weak transcription	Brain Angular Gyrus	brain
30	chr7:138194000-138212000	Weak transcription	NHDF-Ad	bronchial
31	chr7:138194800-138203800	Weak transcription	Right Ventricle	heart
32	chr7:138195000-138203400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr7:138195000-138203800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr7:138195200-138205600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr7:138195200-138212200	Weak transcription	Colon Smooth Muscle	Colon
36	chr7:138196000-138203400	Weak transcription	HSMMtube	muscle
37	chr7:138196400-138202800	Strong transcription	Primary T cells from cord blood	blood
38	chr7:138196800-138209400	Strong transcription	Dnd41	blood
39	chr7:138197000-138204000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr7:138197000-138216000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr7:138197400-138201200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr7:138197400-138201200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:138197400-138201200	Weak transcription	Fetal Kidney	kidney
44	chr7:138197400-138201200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr7:138197400-138203400	Weak transcription	Lung	lung
46	chr7:138197400-138203800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr7:138197400-138204000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr7:138197400-138204000	Weak transcription	Aorta	Aorta
49	chr7:138197400-138208800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:138197400-138210600	Weak transcription	Rectal Smooth Muscle	rectum

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