Variant report

Variant	rs9943221
Chromosome Location	chr1:151914898-151914899
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151913842..151916280-chr1:151933238..151936084,3	MCF-7	breast:
2	chr1:151914726..151916924-chr1:151917247..151919609,3	MCF-7	breast:
3	chr1:151912762..151919992-chr1:151963219..151969467,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229021	Chromatin interaction
ENSG00000197747	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1038747	0.83[CHB][hapmap]
rs10494270	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10788817	0.91[CHB][hapmap]
rs10788820	0.90[CHB][hapmap]
rs11204906	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11204915	0.91[CHB][hapmap]
rs11204919	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11204920	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11582739	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12083193	0.86[CHB][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12095483	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12116923	0.86[CHB][hapmap]
rs12566232	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1387833	0.95[CHB][hapmap]
rs16833668	0.95[CHB][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16833669	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16833670	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16833728	0.91[CHB][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16833743	0.81[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1844543	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279501	0.91[CHB][hapmap]
rs2279502	0.91[CHB][hapmap];0.83[TSI][hapmap]
rs2337685	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2337686	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2338019	0.81[CHB][hapmap]
rs2338206	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28415528	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2932579	0.95[CHB][hapmap];0.81[GIH][hapmap];0.80[TSI][hapmap]
rs2932580	0.88[ASN][1000 genomes]
rs2932590	0.86[CHB][hapmap];0.80[TSI][hapmap]
rs2999526	0.86[CHB][hapmap];0.81[TSI][hapmap]
rs2999528	0.86[CHB][hapmap];0.81[TSI][hapmap]
rs2999531	0.81[CHB][hapmap];0.81[TSI][hapmap]
rs2999542	0.91[CHB][hapmap];0.81[GIH][hapmap]
rs2999544	0.91[CHB][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs3007670	0.91[CHB][hapmap]
rs3007685	0.91[CHB][hapmap];0.81[GIH][hapmap]
rs3007708	0.81[CHB][hapmap];0.81[TSI][hapmap]
rs3007711	0.91[CHB][hapmap];0.81[GIH][hapmap]
rs34251437	0.80[ASN][1000 genomes]
rs3791153	0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4845713	0.89[CHB][hapmap]
rs4845719	0.84[AMR][1000 genomes]
rs56000812	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56028913	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56078223	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56170235	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56313205	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57674198	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57785325	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58087484	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61814883	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61817695	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61817697	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61817719	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61817720	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61817722	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61817723	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61817724	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61817725	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587632	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587633	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587634	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6587635	0.91[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6587636	0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6587637	0.84[CHB][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6587638	0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6587640	0.86[CHB][hapmap];0.93[TSI][hapmap];0.80[ASN][1000 genomes]
rs6657658	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6659662	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6662602	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6662611	0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6662728	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6663064	0.89[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6672064	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6675930	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6678672	0.86[CHB][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6682605	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6684114	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6684312	0.86[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6686874	0.91[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6690449	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6691212	0.80[ASN][1000 genomes]
rs6693388	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6693396	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6693901	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6695324	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6701374	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6703448	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703465	0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72694840	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7535002	0.87[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7538652	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7541099	0.91[CHB][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7554832	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7554859	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs902313	0.91[CHB][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs971887	0.91[CHB][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9943251	0.81[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription 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	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription 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	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9943221	THEM4	cis	cerebellum	SCAN
rs9943221	S100A10	cis	lymphoblastoid	seeQTL
rs9943221	LCE2D	cis	parietal	SCAN
rs9943221	THEM4	cis	parietal	SCAN
rs9943221	S100A10	cis	cerebellum	SCAN
rs9943221	S100A10	cis	parietal	SCAN
rs9943221	S100A10	cis	multi-tissue	Pritchard
rs9943221	THEM4	cis	multi-tissue	Pritchard
rs9943221	THEM4	cis	lymphoblastoid	seeQTL
rs9943221	LCE2C	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151907000-151917400	Weak transcription	Right Atrium	heart
2	chr1:151907600-151916800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:151908200-151916600	Weak transcription	Placenta	Placenta
4	chr1:151908200-151917000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:151909400-151916800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:151909400-151917000	Weak transcription	Colonic Mucosa	Colon
7	chr1:151909600-151917800	Weak transcription	HUVEC	blood vessel
8	chr1:151909800-151916400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:151911600-151916000	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr1:151912000-151917000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:151912200-151917800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:151912800-151915000	Enhancers	NHLF	lung
13	chr1:151912800-151915600	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr1:151913000-151915000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:151913000-151915000	Enhancers	NHDF-Ad	bronchial
16	chr1:151913000-151917200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:151913000-151919800	Enhancers	Fetal Intestine Large	intestine
18	chr1:151913200-151915000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr1:151913200-151915400	Enhancers	Fetal Intestine Small	intestine
20	chr1:151913200-151915600	Enhancers	Duodenum Mucosa	Duodenum
21	chr1:151913200-151916600	Enhancers	Hela-S3	cervix
22	chr1:151913200-151916800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:151913200-151917800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:151913200-151919000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr1:151913600-151915000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:151913600-151915000	Enhancers	Fetal Lung	lung
27	chr1:151913600-151915600	Enhancers	Ovary	ovary
28	chr1:151913800-151917000	Enhancers	Adipose Nuclei	Adipose
29	chr1:151914000-151915000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:151914000-151916000	Weak transcription	Left Ventricle	heart
31	chr1:151914000-151916600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:151914000-151917000	Weak transcription	Esophagus	oesophagus
33	chr1:151914000-151917000	Weak transcription	Psoas Muscle	Psoas
34	chr1:151914000-151917000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:151914000-151917400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:151914000-151922000	Weak transcription	Spleen	Spleen
37	chr1:151914200-151915200	Weak transcription	Fetal Heart	heart
38	chr1:151914200-151915400	Weak transcription	K562	blood
39	chr1:151914200-151915600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr1:151914200-151916800	Weak transcription	HSMM	muscle
41	chr1:151914200-151917000	Weak transcription	Pancreas	Pancrea
42	chr1:151914200-151917400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:151914200-151917800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr1:151914400-151915400	Weak transcription	Fetal Kidney	kidney
45	chr1:151914400-151915600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr1:151914400-151916400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:151914400-151916800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:151914400-151917000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:151914400-151917200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:151914400-151917200	Weak transcription	HSMMtube	muscle

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