Variant report

Variant	rs1993818
Chromosome Location	chr11:10540331-10540332
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr11:10540291-10540584	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:10534893..10539429-chr11:10540096..10542426,4	K562	blood:
2	chr11:10538298..10540845-chr11:10561134..10562717,2	MCF-7	breast:

Variant related genes	Relation type
RNF141	TF binding region
ENSG00000110315	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10219205	0.82[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs10437597	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10500726	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1065052	0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1074375	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1074377	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770123	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840431	0.85[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10840435	0.88[ASN][1000 genomes]
rs10840436	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10840438	0.82[CEU][hapmap]
rs10840441	0.82[TSI][hapmap]
rs12277871	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12279850	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531479	0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs16907989	0.82[CEU][hapmap]
rs1870951	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1993817	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993819	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054392	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2071018	0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34466373	0.98[ASN][1000 genomes]
rs3741034	0.87[TSI][hapmap]
rs3741037	0.84[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs3741038	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3741039	0.93[ASN][1000 genomes]
rs3741041	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3781863	0.88[ASN][1000 genomes]
rs4910146	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4910153	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6484344	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7941294	0.88[EUR][1000 genomes]
rs7951653	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv1044011	chr11:10529353-10564450	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv819964	chr11:10537254-10545535	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1993818	RNF141	cis	parietal	SCAN
rs1993818	GALNTL4	cis	cerebellum	SCAN
rs1993818	SNORA45	cis	cerebellum	SCAN
rs1993818	MICAL2	cis	parietal	SCAN
rs1993818	MRVI1	cis	normal skin	skin_eQTL
rs1993818	AMPD3	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10501600-10550600	Weak transcription	Small Intestine	intestine
2	chr11:10502600-10560800	Weak transcription	Fetal Brain Male	brain
3	chr11:10507800-10544800	Weak transcription	Fetal Kidney	kidney
4	chr11:10512800-10540400	Weak transcription	Fetal Lung	lung
5	chr11:10512800-10548600	Weak transcription	Right Ventricle	heart
6	chr11:10515800-10540600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:10516000-10544000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr11:10520000-10543400	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:10522200-10541200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:10522400-10540600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr11:10522400-10546200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr11:10522400-10560800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:10522800-10540600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr11:10524600-10540600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr11:10524600-10544800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:10525800-10555600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr11:10526400-10548800	Weak transcription	Spleen	Spleen
18	chr11:10526400-10549000	Weak transcription	Ovary	ovary
19	chr11:10526400-10551800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:10526400-10561600	Weak transcription	Colonic Mucosa	Colon
21	chr11:10526800-10548800	Weak transcription	Psoas Muscle	Psoas
22	chr11:10527200-10540600	Weak transcription	Gastric	stomach
23	chr11:10527600-10542400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr11:10527800-10541000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr11:10528000-10540400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr11:10528000-10540600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr11:10528000-10540600	Weak transcription	Fetal Muscle Leg	muscle
28	chr11:10528000-10542600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:10528400-10548800	Weak transcription	K562	blood
30	chr11:10528400-10550600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:10528400-10555800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr11:10528600-10541000	Weak transcription	Brain Anterior Caudate	brain
33	chr11:10529200-10541000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr11:10532600-10540400	Weak transcription	Placenta	Placenta
35	chr11:10533200-10540400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr11:10533200-10541000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:10533200-10542800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr11:10533200-10549000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:10533200-10552000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr11:10533200-10561600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr11:10533200-10561600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr11:10533400-10541000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr11:10533400-10561400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr11:10533600-10541000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:10533600-10543400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr11:10533600-10543800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr11:10533800-10543800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr11:10533800-10557400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr11:10534000-10541200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr11:10534800-10540600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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