Variant report

Variant	rs7283707
Chromosome Location	chr21:17126994-17126995
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:17101896..17103762-chr21:17124530..17127504,2	MCF-7	breast:
2	chr21:17102136..17104047-chr21:17126942..17128676,2	K562	blood:
3	chr21:17125329..17127564-chr21:17142354..17143881,2	K562	blood:
4	chr21:17102350..17105296-chr21:17124464..17127138,3	MCF-7	breast:
5	chr21:17116180..17118994-chr21:17126178..17127711,2	K562	blood:
6	chr21:17125584..17127953-chr21:17130378..17132537,2	K562	blood:
7	chr21:17126721..17128269-chr21:17130491..17133281,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155313	Chromatin interaction
ENSG00000234159	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10482875	0.83[CEU][hapmap]
rs10482876	1.00[CEU][hapmap]
rs11910884	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs11911814	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1543299	0.91[CEU][hapmap]
rs17241416	1.00[CEU][hapmap]
rs17241423	1.00[CEU][hapmap]
rs17241430	1.00[CEU][hapmap]
rs17241444	1.00[CEU][hapmap]
rs17307120	0.83[CEU][hapmap]
rs17307176	1.00[CEU][hapmap]
rs1986788	0.81[AFR][1000 genomes]
rs1989381	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2026853	0.94[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.93[YRI][hapmap]
rs2205585	0.85[AFR][1000 genomes]
rs2205589	0.81[AFR][1000 genomes]
rs2223176	0.85[AFR][1000 genomes]
rs2242676	1.00[CEU][hapmap]
rs2245574	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs2404001	0.83[CEU][hapmap]
rs2823455	0.91[CEU][hapmap]
rs2823462	0.83[CEU][hapmap]
rs2823463	0.83[CEU][hapmap]
rs2823467	0.82[AFR][1000 genomes]
rs2823469	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2823470	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2823471	1.00[CEU][hapmap]
rs2823472	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823473	0.85[AFR][1000 genomes]
rs2823476	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2823477	0.82[YRI][hapmap]
rs2823478	1.00[CEU][hapmap]
rs2823482	0.89[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2823487	0.82[YRI][hapmap]
rs2823489	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2823491	1.00[CEU][hapmap]
rs2823493	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs2823495	0.83[AFR][1000 genomes]
rs2823496	0.85[AFR][1000 genomes]
rs2823497	0.87[AFR][1000 genomes]
rs2823499	0.89[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs2823500	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[YRI][hapmap]
rs2823504	0.91[CEU][hapmap]
rs28627435	0.85[AFR][1000 genomes]
rs28725201	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28730511	0.87[AFR][1000 genomes]
rs3787577	1.00[CEU][hapmap]
rs6517609	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6517611	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6517612	0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes]
rs6517613	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6517648	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6517652	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs722887	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7277807	0.83[CEU][hapmap]
rs7277813	0.84[AFR][1000 genomes]
rs7278428	0.83[CEU][hapmap]
rs7279157	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7279170	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7281511	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs7283764	0.83[CEU][hapmap]
rs73346766	0.82[AFR][1000 genomes]
rs8127158	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8130607	0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes]
rs8134327	1.00[ASW][hapmap];0.91[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs926612	1.00[MEX][hapmap]
rs9941829	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9974210	0.87[AFR][1000 genomes]
rs9976815	0.82[AFR][1000 genomes]
rs9977000	0.87[AFR][1000 genomes]
rs9981766	0.85[AFR][1000 genomes]
rs9982083	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9982479	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9983248	0.81[AFR][1000 genomes]
rs9983458	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762093	chr21:16948663-17145770	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1064683	chr21:16954570-17145758	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv459099	chr21:16956866-17145011	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv587076	chr21:16956866-17145011	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1062105	chr21:16956885-17141961	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv544380	chr21:16956885-17141961	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1059500	chr21:16957752-17145758	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv1815433	chr21:17106192-17167353	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv275197	chr21:17123855-17130358	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7283707	MSX1	trans	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17104200-17133400	Weak transcription	Colonic Mucosa	Colon
2	chr21:17115200-17130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr21:17115400-17145400	Weak transcription	Fetal Thymus	thymus
4	chr21:17115600-17133400	Weak transcription	Dnd41	blood
5	chr21:17115600-17139400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr21:17116200-17139400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr21:17116600-17145400	Weak transcription	Esophagus	oesophagus
8	chr21:17122200-17127200	Enhancers	Psoas Muscle	Psoas
9	chr21:17122200-17129200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr21:17122600-17129000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr21:17122600-17142800	Weak transcription	Hela-S3	cervix
12	chr21:17123400-17128000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr21:17123400-17128200	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr21:17123400-17129400	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr21:17123400-17129400	Enhancers	Small Intestine	intestine
16	chr21:17123400-17130200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr21:17123600-17133000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr21:17124800-17127200	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr21:17124800-17127200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr21:17124800-17127400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr21:17124800-17127800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr21:17124800-17128000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr21:17124800-17128800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr21:17124800-17129200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr21:17124800-17129400	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr21:17124800-17130200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr21:17124800-17130200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr21:17125000-17127000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr21:17125000-17127600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr21:17125000-17127800	Enhancers	HMEC	breast
31	chr21:17125000-17128000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr21:17125000-17128000	Enhancers	Colon Smooth Muscle	Colon
33	chr21:17125000-17128000	Enhancers	HepG2	liver
34	chr21:17125000-17129800	Enhancers	HUVEC	blood vessel
35	chr21:17125200-17127000	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr21:17125200-17127200	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr21:17125200-17127200	Enhancers	Primary B cells from peripheral blood	blood
38	chr21:17125200-17127400	Enhancers	Brain Substantia Nigra	brain
39	chr21:17125200-17127400	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr21:17125200-17128000	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr21:17125200-17129400	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr21:17125400-17127000	Enhancers	Brain Hippocampus Middle	brain
43	chr21:17125400-17127200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr21:17125400-17127800	Enhancers	Fetal Intestine Large	intestine
45	chr21:17125600-17127600	Enhancers	Fetal Intestine Small	intestine
46	chr21:17125600-17129400	Enhancers	H1 Cell Line	embryonic stem cell
47	chr21:17125800-17133600	Weak transcription	Lung	lung
48	chr21:17125800-17153400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr21:17126000-17127800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr21:17126200-17127400	Enhancers	NHDF-Ad	bronchial

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