Variant report

Variant	rs28616724
Chromosome Location	chr14:69845593-69845594
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:69839397..69841083-chr14:69844631..69847497,2	MCF-7	breast:
2	chr14:69841356..69843635-chr14:69843836..69846318,2	K562	blood:
3	chr14:69841304..69844140-chr14:69845246..69848193,3	K562	blood:
4	chr14:69843804..69846515-chr14:69848957..69850700,2	MCF-7	breast:
5	chr14:69824235..69826782-chr14:69843380..69845607,3	MCF-7	breast:
6	chr14:69842726..69844478-chr14:69844525..69846772,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1010661	0.80[CEU][hapmap]
rs10130642	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10131686	0.93[AMR][1000 genomes]
rs10132626	0.85[CHD][hapmap];0.93[LWK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10137655	0.81[ASW][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes]
rs10137668	0.90[ASW][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes]
rs10142738	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10148090	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10150434	0.93[AMR][1000 genomes]
rs11158808	0.82[MEX][hapmap];0.82[TSI][hapmap]
rs11620664	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622130	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624753	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624756	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11626070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11844803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11847666	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12147167	0.93[AMR][1000 genomes]
rs12147983	0.93[AMR][1000 genomes]
rs12147999	0.93[AMR][1000 genomes]
rs12185028	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12385913	1.00[ASW][hapmap];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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17106979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17764155	1.00[CHD][hapmap];0.95[LWK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1952255	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2015547	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2061087	0.82[MEX][hapmap]
rs2061088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28531897	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs35286134	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36088452	0.81[AFR][1000 genomes]
rs45536240	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55751520	0.93[AMR][1000 genomes]
rs57148905	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57675317	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57941356	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59116152	0.93[AMR][1000 genomes]
rs59181716	0.93[AMR][1000 genomes]
rs60238702	0.93[AMR][1000 genomes]
rs61436917	0.93[AMR][1000 genomes]
rs61564515	0.93[AMR][1000 genomes]
rs7143230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7152301	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7155178	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7161463	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs72722198	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72722199	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72723815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723830	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723840	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723847	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72723850	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723857	0.93[AMR][1000 genomes]
rs74061833	0.89[AMR][1000 genomes]
rs8016334	0.91[ASN][1000 genomes]
rs8016618	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630395	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28616724	GALNTL1	cis	cerebellum	SCAN
rs28616724	ADAM21	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69821800-69852400	Weak transcription	Spleen	Spleen
2	chr14:69824200-69864000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:69830000-69847200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr14:69831200-69852400	Weak transcription	Brain Substantia Nigra	brain
5	chr14:69833200-69845600	Weak transcription	Fetal Stomach	stomach
6	chr14:69835400-69851800	Weak transcription	Psoas Muscle	Psoas
7	chr14:69835600-69851600	Weak transcription	Pancreas	Pancrea
8	chr14:69835800-69852400	Weak transcription	Small Intestine	intestine
9	chr14:69836800-69851600	Weak transcription	Gastric	stomach
10	chr14:69837000-69845800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr14:69837200-69860000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr14:69837400-69851000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr14:69838000-69846200	Weak transcription	Esophagus	oesophagus
14	chr14:69839200-69852200	Weak transcription	Aorta	Aorta
15	chr14:69839800-69851600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr14:69840800-69851600	Weak transcription	Colonic Mucosa	Colon
17	chr14:69840800-69852400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr14:69841000-69863400	Strong transcription	A549	lung
19	chr14:69841200-69863000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr14:69841400-69847800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr14:69841400-69862800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr14:69841600-69848600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr14:69841600-69858000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr14:69841600-69863400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr14:69841800-69848400	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr14:69841800-69849800	Strong transcription	Duodenum Mucosa	Duodenum
27	chr14:69841800-69857800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr14:69841800-69863000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr14:69841800-69863800	Weak transcription	Stomach Mucosa	stomach
30	chr14:69842000-69851400	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr14:69842000-69852400	Weak transcription	Fetal Brain Male	brain
32	chr14:69842000-69858600	Weak transcription	Fetal Heart	heart
33	chr14:69842200-69846800	Strong transcription	NHEK	skin
34	chr14:69842200-69847800	Strong transcription	Thymus	Thymus
35	chr14:69842200-69857800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr14:69842400-69846600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr14:69842400-69849000	Strong transcription	HepG2	liver
38	chr14:69842400-69854400	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr14:69842600-69848400	Strong transcription	Placenta	Placenta
40	chr14:69842600-69863200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr14:69842800-69854800	Strong transcription	Primary T cells from cord blood	blood
42	chr14:69842800-69857800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr14:69842800-69862800	Strong transcription	Fetal Thymus	thymus
44	chr14:69843000-69847400	Strong transcription	GM12878-XiMat	blood
45	chr14:69843000-69848000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr14:69843000-69854000	Strong transcription	Hela-S3	cervix
47	chr14:69843200-69846400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr14:69843400-69856600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr14:69843400-69863000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr14:69843600-69845600	Weak transcription	Colon Smooth Muscle	Colon

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