Variant report

Variant	rs11075910
Chromosome Location	chr16:71936733-71936734
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71936147..71938955-chr16:71940995..71943560,3	K562	blood:
2	chr16:71926844..71931687-chr16:71933054..71938868,11	MCF-7	breast:
3	chr16:71935084..71939148-chr16:71940742..71943811,5	MCF-7	breast:
4	chr16:71933462..71935893-chr16:71936421..71939134,2	MCF-7	breast:
5	chr16:71935199..71937559-chr16:71949615..71951829,2	MCF-7	breast:
6	chr16:71933405..71937193-chr16:71939159..71943581,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102984	Chromatin interaction
ENSG00000182149	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10500567	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs10852505	1.00[CHB][hapmap]
rs11639902	1.00[CHB][hapmap]
rs11642529	1.00[CHB][hapmap]
rs11644740	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11648557	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11865456	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12149307	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12149325	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12444594	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12445564	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12445641	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12447045	0.93[YRI][hapmap]
rs12708918	0.86[EUR][1000 genomes]
rs12708919	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs12934512	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs13332180	0.82[ASW][hapmap]
rs17286411	0.94[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs17357420	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs17358402	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1834036	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2288030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2878494	1.00[CHB][hapmap]
rs35619990	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3751820	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4528577	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4538017	0.82[ASW][hapmap]
rs4788450	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs4788561	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4788567	0.82[ASW][hapmap]
rs4788568	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][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];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788569	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788575	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4788579	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs7188591	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7195988	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7197486	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7198834	0.85[JPT][hapmap]
rs7202840	1.00[CHB][hapmap]
rs8044004	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8044335	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8050058	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs8051878	1.00[CHB][hapmap]
rs8052358	0.85[JPT][hapmap]
rs8055655	0.82[ASN][1000 genomes]
rs9932707	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9939911	0.85[JPT][hapmap]
rs9940234	1.00[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv1056439	chr16:71916498-72051144	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv906893	chr16:71922663-71988728	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11075910	MTSS1L	cis	parietal	SCAN
rs11075910	AARS	cis	parietal	SCAN
rs11075910	MARVELD3	cis	lymphoblastoid	seeQTL
rs11075910	PDXDC2P	cis	cerebellum	SCAN
rs11075910	HPR	cis	cerebellum	SCAN
rs11075910	TMEM208	cis	parietal	SCAN
rs11075910	PSMD7	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71930800-71943200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr16:71930800-71944200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr16:71930800-71950000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:71930800-71951800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr16:71931000-71937000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr16:71931000-71937800	Enhancers	Primary B cells from peripheral blood	blood
7	chr16:71931000-71942800	Weak transcription	Fetal Heart	heart
8	chr16:71931000-71949400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr16:71931000-71949600	Weak transcription	NHEK	skin
10	chr16:71931200-71936800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr16:71931200-71936800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr16:71931200-71936800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr16:71931200-71937000	Weak transcription	Brain Germinal Matrix	brain
14	chr16:71931200-71938200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr16:71931200-71940600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr16:71931200-71942800	Weak transcription	HSMM	muscle
17	chr16:71931200-71943000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr16:71931200-71943000	Weak transcription	Fetal Lung	lung
19	chr16:71931200-71943000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr16:71931200-71943200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr16:71931200-71944800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr16:71931200-71946600	Weak transcription	A549	lung
23	chr16:71931200-71949800	Weak transcription	Esophagus	oesophagus
24	chr16:71931200-71950000	Weak transcription	HMEC	breast
25	chr16:71931200-71956200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr16:71931400-71942600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr16:71931400-71949400	Weak transcription	Fetal Kidney	kidney
28	chr16:71931600-71937200	Weak transcription	Fetal Intestine Large	intestine
29	chr16:71931600-71942400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr16:71931600-71944400	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr16:71932000-71942600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr16:71932000-71942600	Weak transcription	Thymus	Thymus
33	chr16:71932000-71942800	Weak transcription	Hela-S3	cervix
34	chr16:71932000-71943200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr16:71932400-71937000	Weak transcription	Pancreas	Pancrea
36	chr16:71932400-71943000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr16:71932600-71942600	Weak transcription	Gastric	stomach
38	chr16:71932600-71951800	Weak transcription	Colonic Mucosa	Colon
39	chr16:71932800-71942600	Weak transcription	Fetal Thymus	thymus
40	chr16:71933200-71942600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr16:71933400-71937600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr16:71933400-71938000	Weak transcription	Spleen	Spleen
43	chr16:71933400-71940400	Weak transcription	Fetal Muscle Leg	muscle
44	chr16:71933400-71942600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr16:71933400-71948400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr16:71933400-71949000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr16:71933400-71950200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr16:71933600-71938000	Weak transcription	Fetal Intestine Small	intestine
49	chr16:71933600-71938000	Weak transcription	Fetal Stomach	stomach
50	chr16:71934000-71938200	Weak transcription	Left Ventricle	heart

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