Variant report

Variant	rs12983047
Chromosome Location	chr19:41834499-41834500
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41831560..41835425-chr19:41857306..41860915,5	MCF-7	breast:
2	chr19:41831768..41836591-chr19:41855042..41861850,7	MCF-7	breast:
3	chr19:41828482..41836150-chr19:41836490..41842395,12	K562	blood:
4	chr19:41832909..41835024-chr19:42101795..42103812,2	MCF-7	breast:
5	chr19:41833038..41835641-chr19:41836593..41839563,3	MCF-7	breast:
6	chr19:41832250..41834586-chr19:41869833..41871949,2	MCF-7	breast:
7	chr19:41833143..41834852-chr19:41837091..41839256,2	MCF-7	breast:
8	chr19:41831346..41834829-chr19:41839847..41842634,3	MCF-7	breast:
9	chr19:41832138..41834611-chr19:41867013..41869062,2	K562	blood:
10	chr19:41827333..41835079-chr19:41855373..41860241,10	K562	blood:
11	chr19:41769289..41771419-chr19:41832191..41834846,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000123810	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000255730	Chromatin interaction
ENSG00000142046	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10410836	0.96[ASN][1000 genomes]
rs10421990	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.99[ASN][1000 genomes]
rs1056854	0.91[CEU][hapmap]
rs11466347	0.95[EUR][1000 genomes]
rs11466359	0.86[EUR][1000 genomes]
rs11879562	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11880564	0.86[EUR][1000 genomes]
rs11881940	0.91[CEU][hapmap]
rs11882467	0.90[CHB][hapmap]
rs12327659	0.86[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.83[YRI][hapmap];0.99[ASN][1000 genomes]
rs12462203	0.85[CHB][hapmap]
rs12972266	0.81[EUR][1000 genomes]
rs12972949	0.86[EUR][1000 genomes]
rs12974323	0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12974420	0.91[CEU][hapmap]
rs12975585	0.90[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs12975920	0.98[ASN][1000 genomes]
rs12978323	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs12980298	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12980480	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12980839	0.95[ASN][1000 genomes]
rs12980942	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12981053	0.98[EUR][1000 genomes]
rs12984160	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12985162	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs12985339	0.91[CEU][hapmap]
rs13345456	0.99[ASN][1000 genomes]
rs16958994	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16958996	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16958999	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16959007	0.83[YRI][hapmap]
rs16975124	0.87[YRI][hapmap]
rs16975156	0.83[YRI][hapmap]
rs16975164	0.87[YRI][hapmap]
rs1865051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1865052	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1865053	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2053086	0.91[CEU][hapmap]
rs2241718	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2241719	0.86[EUR][1000 genomes]
rs2241720	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2304230	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.88[YRI][hapmap];0.96[ASN][1000 genomes]
rs2304234	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs34075897	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34322801	0.81[EUR][1000 genomes]
rs34945449	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35501756	0.82[EUR][1000 genomes]
rs3745295	0.86[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes]
rs3752705	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3810173	0.82[YRI][hapmap]
rs3816052	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.96[ASN][1000 genomes]
rs3826714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4456618	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4802111	0.85[CHB][hapmap]
rs4802112	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs4802113	0.84[CHB][hapmap]
rs4803448	0.85[CHB][hapmap]
rs4803449	0.85[CHB][hapmap]
rs61459202	0.86[EUR][1000 genomes]
rs6508974	0.85[CHB][hapmap]
rs66724427	0.96[ASN][1000 genomes]
rs67511749	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6957	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7245398	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7246525	0.85[CHB][hapmap]
rs7248164	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.99[ASN][1000 genomes]
rs7254679	0.82[CEU][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7256416	0.96[ASN][1000 genomes]
rs7256856	0.94[ASN][1000 genomes]
rs7257310	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257742	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257825	0.95[ASN][1000 genomes]
rs7258749	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs747857	0.83[YRI][hapmap]
rs8103839	0.91[CEU][hapmap]
rs8105161	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8105901	0.91[CEU][hapmap]
rs8109167	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109627	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs998468	0.83[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911769	chr19:41813676-41845801	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12983047	TSKS	cis	parietal	SCAN
rs12983047	BAX	cis	cerebellum	SCAN
rs12983047	PLEKHA4	cis	cerebellum	SCAN
rs12983047	FLT3LG	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41818600-41854800	Strong transcription	Dnd41	blood
2	chr19:41829200-41835400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr19:41830800-41834600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr19:41830800-41835000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:41831600-41835200	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr19:41831600-41835400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr19:41831800-41834600	Enhancers	Fetal Heart	heart
8	chr19:41831800-41835200	Genic enhancers	Spleen	Spleen
9	chr19:41832000-41835200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr19:41832200-41835000	Enhancers	Left Ventricle	heart
11	chr19:41832200-41835200	Genic enhancers	A549	lung
12	chr19:41832200-41835200	Genic enhancers	K562	blood
13	chr19:41832400-41834800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:41832400-41835000	Enhancers	Brain Angular Gyrus	brain
15	chr19:41832400-41835000	Genic enhancers	HSMM	muscle
16	chr19:41832400-41835200	Enhancers	Liver	Liver
17	chr19:41832400-41835200	Flanking Active TSS	Colonic Mucosa	Colon
18	chr19:41832400-41835400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:41832400-41837000	Weak transcription	Ovary	ovary
20	chr19:41832400-41856000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr19:41832600-41834800	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr19:41832600-41836600	Weak transcription	Aorta	Aorta
23	chr19:41832600-41837000	Weak transcription	Colon Smooth Muscle	Colon
24	chr19:41832600-41837600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr19:41833000-41834600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
26	chr19:41833000-41834600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr19:41833000-41834800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr19:41833200-41834800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
29	chr19:41833400-41837000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr19:41833400-41846400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:41833600-41834800	Enhancers	Brain Cingulate Gyrus	brain
32	chr19:41833600-41835000	Genic enhancers	Fetal Thymus	thymus
33	chr19:41833600-41835200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr19:41833600-41835200	Genic enhancers	NHLF	lung
35	chr19:41833600-41835400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr19:41833600-41836400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr19:41833800-41834600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr19:41833800-41834800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr19:41833800-41835000	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr19:41833800-41835000	Enhancers	H1 Cell Line	embryonic stem cell
41	chr19:41833800-41835000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
42	chr19:41833800-41835000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:41833800-41835000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr19:41833800-41835000	Genic enhancers	Fetal Stomach	stomach
45	chr19:41833800-41835200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
46	chr19:41833800-41835200	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr19:41833800-41835200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:41833800-41835200	Genic enhancers	Muscle Satellite Cultured Cells	--
49	chr19:41833800-41835400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:41833800-41837000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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