Variant report

Variant	rs6972821
Chromosome Location	chr7:27879473-27879474
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:27870030..27872206-chr7:27878302..27880164,2	MCF-7	breast:
2	chr7:27874082..27877005-chr7:27878628..27880591,4	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10155851	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10225487	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10267854	0.82[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10277437	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10486559	0.95[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10951184	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16874364	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16874393	0.86[CEU][hapmap];0.82[CHB][hapmap]
rs16874395	0.86[CEU][hapmap]
rs17150563	0.80[EUR][1000 genomes]
rs17155702	0.95[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17155943	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17155950	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs17155969	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs17155971	0.82[CEU][hapmap]
rs2051830	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2074579	0.95[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2074769	0.95[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2107413	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2108309	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2158388	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2237339	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2237340	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2237341	0.91[EUR][1000 genomes]
rs2285930	0.80[MEX][hapmap];0.83[TSI][hapmap]
rs2285931	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2299106	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2391450	0.82[CEU][hapmap]
rs2391488	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3779473	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3940270	0.89[CEU][hapmap];0.82[AMR][1000 genomes]
rs4719907	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4719908	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4722741	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57932688	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58314651	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62449629	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62449639	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62449640	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62451077	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62451079	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62454806	0.85[EUR][1000 genomes]
rs62454945	0.84[EUR][1000 genomes]
rs6462048	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6462049	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6462052	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6462053	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6944251	0.95[CEU][hapmap];0.82[CHB][hapmap];0.90[EUR][1000 genomes]
rs6944913	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6971813	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72598505	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs759268	0.91[CEU][hapmap]
rs7784038	0.82[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7801301	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7803019	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7803227	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7809735	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1028469	chr7:27767795-27939667	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2758109	chr7:27793616-27972869	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv2759520	chr7:27793616-27972869	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv5677	chr7:27839504-27884505	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1018550	chr7:27844038-27925645	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6972821	KCNA2	trans	parietal	SCAN
rs6972821	TAX1BP1	Cis_1M	lymphoblastoid	RTeQTL
rs6972821	CRHR2	cis	parietal	SCAN
rs6972821	SNX10	cis	cerebellum	SCAN
rs6972821	SCRN1	cis	cerebellum	SCAN
rs6972821	TAX1BP1	cis	cerebellum	SCAN
rs6972821	PRR15	cis	parietal	SCAN
rs6972821	HOXA13	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27806000-27882600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:27827000-27881800	Weak transcription	Small Intestine	intestine
3	chr7:27836400-27882200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr7:27840000-27880600	Weak transcription	Hela-S3	cervix
5	chr7:27847600-27885200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr7:27850200-27881400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:27854200-27882200	Weak transcription	Brain Substantia Nigra	brain
8	chr7:27856000-27882200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:27858200-27882600	Weak transcription	Esophagus	oesophagus
10	chr7:27858400-27879600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:27858600-27880000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr7:27858800-27879800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr7:27858800-27880200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr7:27860000-27881800	Weak transcription	Colonic Mucosa	Colon
15	chr7:27861400-27880800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr7:27862000-27881000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr7:27866000-27884600	Strong transcription	Primary B cells from cord blood	blood
18	chr7:27866200-27882200	Weak transcription	NHLF	lung
19	chr7:27866600-27879800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr7:27866800-27880000	Weak transcription	Aorta	Aorta
21	chr7:27868600-27879600	Weak transcription	Fetal Muscle Leg	muscle
22	chr7:27869000-27879600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr7:27869000-27879600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr7:27869600-27882800	Strong transcription	Primary B cells from peripheral blood	blood
25	chr7:27869800-27879600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr7:27870600-27891800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr7:27870800-27882200	Weak transcription	Brain Germinal Matrix	brain
28	chr7:27871400-27889600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr7:27872000-27881800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr7:27872200-27881600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr7:27872600-27879600	Weak transcription	Fetal Thymus	thymus
32	chr7:27872800-27881400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr7:27872800-27881800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr7:27872800-27881800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr7:27872800-27882000	Weak transcription	Liver	Liver
36	chr7:27872800-27886000	Weak transcription	HMEC	breast
37	chr7:27872800-27890000	Weak transcription	Fetal Lung	lung
38	chr7:27873000-27882600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr7:27873800-27879600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr7:27873800-27879800	Weak transcription	Placenta	Placenta
41	chr7:27873800-27886200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr7:27874000-27883200	Strong transcription	Fetal Stomach	stomach
43	chr7:27874200-27880000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr7:27874200-27881000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr7:27874200-27881400	Weak transcription	NH-A	brain
46	chr7:27874200-27882000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr7:27874200-27882000	Weak transcription	HSMMtube	muscle
48	chr7:27874400-27879600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr7:27874400-27879600	Weak transcription	HSMM	muscle
50	chr7:27874400-27879800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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