Variant report

Variant	rs16948914
Chromosome Location	chr18:44674094-44674095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:44673432..44675834-chr18:44691617..44693277,2	MCF-7	breast:
2	chr18:44664428..44666267-chr18:44672303..44675573,3	K562	blood:
3	chr18:44656520..44659372-chr18:44673623..44675752,2	K562	blood:
4	chr18:44663118..44666144-chr18:44673724..44676472,4	K562	blood:

Variant related genes	Relation type
ENSG00000267800	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10083937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10520715	0.81[CHB][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap]
rs11082563	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11082564	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11872531	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11873880	1.00[AFR][1000 genomes]
rs11875768	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11876448	0.96[ASN][1000 genomes]
rs12326122	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12326221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12326412	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12326457	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12326465	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12326600	0.83[ASN][1000 genomes]
rs12386076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12386092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12386097	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13547	1.00[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[ASN][1000 genomes]
rs1434528	1.00[ASW][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs16948928	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16949157	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16949275	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16950217	0.85[CEU][hapmap]
rs16952848	0.85[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16958432	1.00[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16958440	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16958699	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16958701	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17784414	0.80[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs17784795	0.81[CHB][hapmap];1.00[GIH][hapmap]
rs2117373	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289130	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2289131	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2289132	1.00[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs28578518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28587821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3809965	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3809966	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4609941	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56395942	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs57468764	0.95[ASN][1000 genomes]
rs57744138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57928699	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58061761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59217333	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60228288	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs60422392	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs60726022	0.91[AFR][1000 genomes]
rs60854219	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61316646	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs61689863	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62095459	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62096462	0.95[ASN][1000 genomes]
rs62096463	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs62096464	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs62096465	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62096466	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs62096468	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62096469	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62096470	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62096471	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62096474	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62096477	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs62096478	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72907280	1.00[AFR][1000 genomes]
rs998818	1.00[GIH][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	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv833640	chr18:44552276-44714872	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv909612	chr18:44560875-44681485	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv576819	chr18:44602249-44677627	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv909613	chr18:44644530-44690107	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16948914	HDHD2	cis	lymphoblastoid	seeQTL
rs16948914	HDHD2	cis	multi-tissue	Pritchard
rs16948914	HDHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44620800-44675400	Weak transcription	A549	lung
2	chr18:44621600-44674400	Weak transcription	Small Intestine	intestine
3	chr18:44629200-44675800	Weak transcription	HUVEC	blood vessel
4	chr18:44632400-44675800	Weak transcription	Stomach Mucosa	stomach
5	chr18:44640600-44675600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr18:44641600-44675800	Weak transcription	Lung	lung
7	chr18:44641800-44674400	Weak transcription	Aorta	Aorta
8	chr18:44641800-44675200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr18:44641800-44675400	Weak transcription	Fetal Intestine Small	intestine
10	chr18:44641800-44675800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr18:44641800-44675800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr18:44642000-44675200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr18:44642200-44674600	Weak transcription	NHEK	skin
14	chr18:44647800-44675800	Weak transcription	Ovary	ovary
15	chr18:44656400-44675200	Weak transcription	Thymus	Thymus
16	chr18:44656800-44675000	Weak transcription	Colon Smooth Muscle	Colon
17	chr18:44656800-44675200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr18:44661200-44675800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr18:44661400-44674800	Weak transcription	Brain Substantia Nigra	brain
20	chr18:44661400-44675400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr18:44661400-44675600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr18:44661600-44674800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr18:44661600-44675600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr18:44661600-44675800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr18:44662200-44675800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr18:44662600-44675200	Weak transcription	Hela-S3	cervix
27	chr18:44662800-44674800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr18:44662800-44674800	Weak transcription	Adipose Nuclei	Adipose
29	chr18:44662800-44675000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr18:44662800-44675200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr18:44662800-44675200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr18:44662800-44675400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr18:44662800-44675400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr18:44662800-44675400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr18:44662800-44675400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr18:44662800-44675400	Weak transcription	HMEC	breast
37	chr18:44662800-44675400	Weak transcription	NHDF-Ad	bronchial
38	chr18:44662800-44675600	Weak transcription	Brain Angular Gyrus	brain
39	chr18:44662800-44675600	Weak transcription	Fetal Muscle Leg	muscle
40	chr18:44662800-44675600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr18:44662800-44675800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr18:44662800-44675800	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr18:44662800-44675800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr18:44662800-44675800	Weak transcription	Brain Anterior Caudate	brain
45	chr18:44662800-44675800	Weak transcription	Placenta	Placenta
46	chr18:44663000-44675000	Weak transcription	GM12878-XiMat	blood
47	chr18:44663000-44675200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr18:44663000-44675200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr18:44663000-44675600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr18:44663200-44675600	Weak transcription	Primary B cells from peripheral blood	blood

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