Variant report

Variant	rs16942032
Chromosome Location	chr16:75692964-75692965
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75654334..75656707-chr16:75691498..75693469,2	K562	blood:
2	chr16:75677843..75679921-chr16:75690407..75692993,2	K562	blood:
3	chr16:75691958..75693608-chr16:75693696..75696714,3	MCF-7	breast:
4	chr16:75681364..75684772-chr16:75690611..75693134,4	K562	blood:

Variant related genes	Relation type
ENSG00000166848	Chromatin interaction
ENSG00000065427	Chromatin interaction
ENSG00000065457	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11556641	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];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12922861	1.00[CEU][hapmap]
rs16940260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16940348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16940362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16940444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16940961	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[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16941287	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941301	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16975847	1.00[CHB][hapmap]
rs2164246	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2550320	1.00[AMR][1000 genomes]
rs2550889	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2550892	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2550893	1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2550897	1.00[AMR][1000 genomes]
rs2550900	1.00[AMR][1000 genomes]
rs2550902	1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2550903	1.00[AMR][1000 genomes]
rs2550906	1.00[AMR][1000 genomes]
rs2550914	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2550915	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2641803	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2641807	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2650410	1.00[AMR][1000 genomes]
rs2650411	1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs2650413	0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2738800	1.00[AMR][1000 genomes]
rs55714466	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55862257	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56030666	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56321575	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60919196	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7194333	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72563121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74024796	1.00[AMR][1000 genomes]
rs74027409	1.00[AMR][1000 genomes]
rs74027420	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs74027421	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs74027424	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs74027425	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs74027427	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs74027428	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs74027431	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs74027432	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs74027433	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs74027436	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74027439	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74027441	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74027443	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053257	1.00[CHD][hapmap]
rs8192515	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs920037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv532562	chr16:75614947-76371158	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1062010	chr16:75628562-75825725	Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers 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 miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1064880	chr16:75628562-75895699	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv542960	chr16:75628562-75895699	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv1065543	chr16:75631306-75800170	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16942032	SCGB1D2	trans	brain	seeQTL
rs16942032	RBMXL3	trans	lymphoblastoid	seeQTL
rs16942032	SCGB2A2	trans	brain	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75684600-75695400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:75686200-75694400	Weak transcription	Right Atrium	heart
3	chr16:75686400-75695800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr16:75686600-75695200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr16:75687000-75693000	Strong transcription	K562	blood
6	chr16:75687000-75695400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr16:75687400-75693000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr16:75687400-75693600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr16:75687400-75696000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr16:75687600-75693600	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr16:75687600-75694200	Strong transcription	Fetal Muscle Leg	muscle
12	chr16:75687600-75694600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr16:75687600-75695600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr16:75687600-75696000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr16:75687600-75696000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr16:75687600-75696400	Strong transcription	Primary B cells from cord blood	blood
17	chr16:75687600-75696400	Strong transcription	Fetal Stomach	stomach
18	chr16:75687800-75693000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr16:75687800-75693000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr16:75687800-75693400	Strong transcription	Left Ventricle	heart
21	chr16:75687800-75694200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr16:75687800-75694600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr16:75687800-75694800	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr16:75687800-75695400	Strong transcription	Fetal Thymus	thymus
25	chr16:75687800-75695800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr16:75687800-75696200	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr16:75687800-75696200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr16:75688000-75693000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr16:75688000-75693400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr16:75688000-75693800	Strong transcription	Fetal Intestine Large	intestine
31	chr16:75688000-75694000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr16:75688000-75694200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr16:75688000-75694800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr16:75688000-75695200	Strong transcription	Liver	Liver
35	chr16:75688000-75695200	Strong transcription	GM12878-XiMat	blood
36	chr16:75688000-75695800	Strong transcription	Placenta	Placenta
37	chr16:75688200-75693000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr16:75688200-75693000	Strong transcription	Brain Substantia Nigra	brain
39	chr16:75688200-75693600	Strong transcription	NH-A	brain
40	chr16:75688200-75693800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr16:75688200-75693800	Strong transcription	Brain Germinal Matrix	brain
42	chr16:75688200-75695800	Strong transcription	Primary T cells from cord blood	blood
43	chr16:75688200-75696000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr16:75688200-75696000	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr16:75688400-75693000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr16:75688400-75693000	Strong transcription	Duodenum Mucosa	Duodenum
47	chr16:75688400-75693000	Strong transcription	HSMM	muscle
48	chr16:75688400-75693600	Strong transcription	Dnd41	blood
49	chr16:75688400-75693800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr16:75688400-75693800	Strong transcription	Brain Inferior Temporal Lobe	brain

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