Variant report

Variant	rs421561
Chromosome Location	chr17:19735944-19735945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19734603..19737057-chr17:19741168..19743468,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000083290	Chromatin interaction
ENSG00000231096	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs115326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs118943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs123081	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs123082	0.97[EUR][1000 genomes]
rs150122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs157387	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs157388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs157389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs157390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs157391	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs157392	0.97[EUR][1000 genomes]
rs157393	1.00[CEU][hapmap]
rs157394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs157395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157397	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs157399	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157400	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157403	1.00[EUR][1000 genomes]
rs157405	1.00[CEU][hapmap]
rs157406	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs157408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166838	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs166839	1.00[EUR][1000 genomes]
rs169460	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs169512	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs169513	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs172186	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs176098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs182214	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs184006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs188138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs192511	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs205087	0.90[ASN][1000 genomes]
rs205088	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs205090	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs205092	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs205093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs205094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs205096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs205097	0.84[EUR][1000 genomes]
rs205098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs205099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs205100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs205103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs205104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs205105	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs205106	0.97[EUR][1000 genomes]
rs205107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs205108	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs205110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs205111	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs205112	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs205113	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2385963	1.00[EUR][1000 genomes]
rs281325	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs281326	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs281327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs281328	0.97[EUR][1000 genomes]
rs281329	0.87[EUR][1000 genomes]
rs281330	1.00[AMR][1000 genomes]
rs281331	0.97[EUR][1000 genomes]
rs281332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs281333	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs281334	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs281336	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs281337	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs281338	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs281339	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs281340	0.94[ASN][1000 genomes]
rs281341	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs281342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs281343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs281344	0.97[EUR][1000 genomes]
rs281345	0.97[EUR][1000 genomes]
rs281346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs281347	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs281348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs281349	0.97[EUR][1000 genomes]
rs281350	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs281351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs281352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs281353	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs281354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs281355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs281356	0.97[EUR][1000 genomes]
rs281365	1.00[EUR][1000 genomes]
rs3098902	0.97[EUR][1000 genomes]
rs3098905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098906	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs3098907	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3098908	0.97[EUR][1000 genomes]
rs3098909	0.97[EUR][1000 genomes]
rs3101810	1.00[CEU][hapmap];0.89[YRI][hapmap];0.97[EUR][1000 genomes]
rs3101811	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3101812	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3101813	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3101814	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[EUR][1000 genomes]
rs3101815	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34372768	1.00[EUR][1000 genomes]
rs367383	1.00[EUR][1000 genomes]
rs379703	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs383948	0.93[EUR][1000 genomes]
rs383951	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs394009	0.92[ASN][1000 genomes]
rs395130	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs445958	0.94[EUR][1000 genomes]
rs4586510	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924800	1.00[EUR][1000 genomes]
rs4925047	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6587203	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7225417	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs917519	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv482398	chr17:19673458-19808039	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1057469	chr17:19696714-19787062	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19673800-19769800	Weak transcription	NH-A	brain
2	chr17:19700400-19745200	Weak transcription	Stomach Mucosa	stomach
3	chr17:19700400-19768400	Weak transcription	Fetal Heart	heart
4	chr17:19700800-19769800	Weak transcription	HSMMtube	muscle
5	chr17:19701000-19743200	Weak transcription	Gastric	stomach
6	chr17:19701000-19743400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr17:19701000-19748600	Weak transcription	Spleen	Spleen
8	chr17:19701000-19753400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr17:19701000-19766200	Weak transcription	Primary B cells from cord blood	blood
10	chr17:19701000-19770000	Weak transcription	Colonic Mucosa	Colon
11	chr17:19701200-19758400	Weak transcription	Small Intestine	intestine
12	chr17:19701800-19742800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr17:19703800-19769800	Weak transcription	Psoas Muscle	Psoas
14	chr17:19704400-19754800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr17:19704400-19770000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr17:19706800-19769800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr17:19712400-19769800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr17:19712600-19742400	Weak transcription	Fetal Kidney	kidney
19	chr17:19712600-19748400	Weak transcription	Fetal Brain Male	brain
20	chr17:19716400-19737000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr17:19717200-19736000	Strong transcription	Adipose Nuclei	Adipose
22	chr17:19724200-19749400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr17:19725400-19768600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr17:19727400-19743200	Weak transcription	Osteobl	bone
25	chr17:19727400-19747600	Weak transcription	NHLF	lung
26	chr17:19727400-19749000	Weak transcription	Aorta	Aorta
27	chr17:19727400-19768800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr17:19727600-19737800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr17:19727600-19749000	Weak transcription	Fetal Thymus	thymus
30	chr17:19727600-19749600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr17:19727800-19769800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr17:19728000-19753800	Weak transcription	Thymus	Thymus
33	chr17:19728000-19770000	Weak transcription	Esophagus	oesophagus
34	chr17:19728200-19769800	Weak transcription	HSMM	muscle
35	chr17:19728200-19770000	Weak transcription	Pancreas	Pancrea
36	chr17:19728400-19745000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr17:19728400-19768800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr17:19728600-19737800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr17:19728600-19740200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr17:19728600-19740800	Weak transcription	Brain Angular Gyrus	brain
41	chr17:19728600-19740800	Weak transcription	NHDF-Ad	bronchial
42	chr17:19728600-19741000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr17:19728600-19742200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr17:19728600-19744000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr17:19728600-19745000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr17:19728600-19748200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr17:19728600-19748400	Weak transcription	Brain Substantia Nigra	brain
48	chr17:19728600-19748600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr17:19728600-19749200	Weak transcription	Right Ventricle	heart
50	chr17:19728600-19756000	Weak transcription	HUVEC	blood vessel

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