Variant report

Variant	rs885683
Chromosome Location	chr19:18244690-18244691
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:18230201..18232157-chr19:18244427..18246391,2	MCF-7	breast:
2	chr19:18244407..18246998-chr19:18260303..18263705,3	K562	blood:

Variant related genes	Relation type
ENSG00000269145	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11554159	0.86[CEU][hapmap];0.85[GIH][hapmap]
rs11666281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11666424	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11666906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11668601	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs273488	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs273492	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs273507	0.81[ASN][1000 genomes]
rs273510	0.81[ASN][1000 genomes]
rs4808114	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4808115	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4808745	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4808751	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56252442	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56345159	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60146811	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66464318	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67234314	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72999447	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72999466	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs874628	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055932	chr19:17923918-18369944	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv543923	chr19:17923918-18369944	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats 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	109 gene(s)	inside rSNPs	diseases
3	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
5	nsv833773	chr19:18152971-18302988	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv911241	chr19:18193191-18304700	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv911242	chr19:18201757-18304700	Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv911243	chr19:18206681-18283501	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv911244	chr19:18206681-18304700	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv911245	chr19:18206681-18338101	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv833774	chr19:18213761-18295329	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	nsv833775	chr19:18213761-18390074	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
13	nsv911246	chr19:18224729-18283501	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv911247	chr19:18224729-18288069	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv911248	chr19:18224729-18338101	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
16	nsv911249	chr19:18224729-18375846	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
17	nsv911250	chr19:18224729-18376522	Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
18	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
19	nsv2429	chr19:18234179-18279381	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
20	nsv911252	chr19:18234588-18338101	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
21	nsv911253	chr19:18240127-18418044	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs885683	KIAA1683	cis	multi-tissue	Pritchard
rs885683	CHRM4	trans	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18230200-18246600	Weak transcription	Hela-S3	cervix
2	chr19:18230200-18247200	Weak transcription	NHEK	skin
3	chr19:18230800-18246200	Strong transcription	Fetal Intestine Small	intestine
4	chr19:18230800-18262000	Weak transcription	Dnd41	blood
5	chr19:18231000-18262200	Weak transcription	HMEC	breast
6	chr19:18231400-18262200	Strong transcription	Primary B cells from peripheral blood	blood
7	chr19:18231400-18262400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr19:18231800-18246200	Strong transcription	Fetal Intestine Large	intestine
9	chr19:18232000-18262200	Strong transcription	Brain Hippocampus Middle	brain
10	chr19:18232200-18246400	Strong transcription	Duodenum Mucosa	Duodenum
11	chr19:18232200-18260000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:18232200-18260000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr19:18232200-18261800	Strong transcription	Fetal Stomach	stomach
14	chr19:18232400-18260600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:18232600-18262200	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr19:18233200-18261800	Strong transcription	Thymus	Thymus
17	chr19:18235400-18261600	Strong transcription	Spleen	Spleen
18	chr19:18235600-18248000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:18235600-18260800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr19:18236200-18245000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:18238400-18245800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:18238400-18258800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr19:18238400-18258800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:18238400-18259400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr19:18238400-18259400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr19:18238400-18261400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr19:18238600-18245200	Strong transcription	Liver	Liver
28	chr19:18238600-18245400	Strong transcription	Stomach Smooth Muscle	stomach
29	chr19:18238600-18245800	Strong transcription	Pancreas	Pancrea
30	chr19:18238600-18248400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:18238600-18250200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:18238600-18259600	Strong transcription	Brain Substantia Nigra	brain
33	chr19:18238600-18259600	Strong transcription	Fetal Muscle Leg	muscle
34	chr19:18238600-18260000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:18238600-18260000	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr19:18238600-18260200	Strong transcription	Fetal Brain Female	brain
37	chr19:18238600-18260600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr19:18238600-18260600	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr19:18238800-18246400	Strong transcription	Colonic Mucosa	Colon
40	chr19:18238800-18246400	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr19:18238800-18246400	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr19:18238800-18247000	Strong transcription	GM12878-XiMat	blood
43	chr19:18238800-18247400	Strong transcription	Primary B cells from cord blood	blood
44	chr19:18238800-18248200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr19:18238800-18248400	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr19:18238800-18249200	Strong transcription	Fetal Thymus	thymus
47	chr19:18238800-18257800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr19:18238800-18258000	Strong transcription	Brain Angular Gyrus	brain
49	chr19:18238800-18258800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr19:18238800-18258800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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