Variant report

Variant	rs429349
Chromosome Location	chr2:7167288-7167289
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:7162976..7165040-chr2:7166130..7169066,2	MCF-7	breast:
2	chr2:7158554..7160902-chr2:7167034..7169770,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11679967	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs11691419	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs177922	0.81[EUR][1000 genomes]
rs1964092	0.91[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2460403	0.83[EUR][1000 genomes]
rs2460406	0.81[EUR][1000 genomes]
rs2460407	0.95[ASN][1000 genomes]
rs309303	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs309305	0.95[ASN][1000 genomes]
rs309308	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309313	0.82[EUR][1000 genomes]
rs309315	0.82[EUR][1000 genomes]
rs309323	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs367495	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs367906	0.91[CEU][hapmap];0.88[MKK][hapmap];0.82[EUR][1000 genomes]
rs368831	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs369808	0.91[CEU][hapmap];0.93[GIH][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs376219	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3771993	0.81[EUR][1000 genomes]
rs377617	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs378548	0.81[EUR][1000 genomes]
rs3821334	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs389351	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs389411	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs392409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392709	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs401164	0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs403196	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs405503	0.81[EUR][1000 genomes]
rs409120	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs410210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs415204	0.91[CEU][hapmap];0.93[GIH][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs416416	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs418312	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs418878	0.82[EUR][1000 genomes]
rs422341	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs425247	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs433983	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs434607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447031	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs447627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs449500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs451763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454999	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs530431	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv526590	chr2:7166507-7167589	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs429349	RNF144A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:7131000-7167600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr2:7148200-7172600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:7148800-7171400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:7151200-7185200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:7152600-7192400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:7154000-7183200	Strong transcription	Primary T cells from cord blood	blood
7	chr2:7154000-7190200	Strong transcription	Dnd41	blood
8	chr2:7154600-7174800	Weak transcription	Primary B cells from cord blood	blood
9	chr2:7154600-7184200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:7155000-7171400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:7155200-7182000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr2:7155600-7178800	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr2:7156000-7168800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:7157000-7177600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:7157000-7179200	Weak transcription	Aorta	Aorta
16	chr2:7157200-7169000	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:7157200-7185200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:7158000-7168400	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr2:7158200-7173200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:7158200-7188800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:7158400-7173000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr2:7158400-7186800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:7158600-7173400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:7159000-7181000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:7159400-7186800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:7159600-7180600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:7160800-7169200	Weak transcription	Placenta	Placenta
28	chr2:7162000-7168400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:7162000-7171600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:7162400-7169800	Weak transcription	Esophagus	oesophagus
31	chr2:7162800-7167400	Genic enhancers	Left Ventricle	heart
32	chr2:7162800-7171400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:7163000-7171000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
34	chr2:7163000-7171400	Weak transcription	Stomach Mucosa	stomach
35	chr2:7163200-7177400	Weak transcription	Fetal Brain Male	brain
36	chr2:7164000-7171200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:7164000-7171600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:7164000-7177600	Weak transcription	NHDF-Ad	bronchial
39	chr2:7164000-7178000	Weak transcription	K562	blood
40	chr2:7164200-7168800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr2:7164600-7167800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:7164600-7171200	Weak transcription	Fetal Intestine Large	intestine
43	chr2:7164600-7182200	Weak transcription	Small Intestine	intestine
44	chr2:7164800-7167400	Genic enhancers	Pancreas	Pancrea
45	chr2:7164800-7189000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr2:7165000-7167800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:7165000-7167800	Genic enhancers	Fetal Kidney	kidney
48	chr2:7165000-7169200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:7165200-7171400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr2:7165400-7168200	Weak transcription	Brain Anterior Caudate	brain

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