Variant report

Variant	rs11876700
Chromosome Location	chr18:9520003-9520004
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:9334537..9336244-chr18:9518482..9520647,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TWSG1-3	chr18:9519447-9520197	ENSG00000273352.1

Variant related genes	Relation type
ENSG00000128791	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12680	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12955301	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958342	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958352	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958901	0.88[EUR][1000 genomes]
rs12962895	0.86[ASN][1000 genomes]
rs12965004	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12965619	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12966136	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12969608	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12970100	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16955222	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16955240	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16955247	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34361892	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34863209	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34870926	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34979461	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35062594	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35189459	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35833761	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36064377	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57539532	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71362083	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7228633	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7231281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7231656	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7232664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7236410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8085681	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8096628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8099656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1062025	chr18:9287249-9552470	Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv543643	chr18:9287249-9552470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv428005	chr18:9401658-9542396	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9478000-9522400	Weak transcription	Hela-S3	cervix
2	chr18:9479000-9533200	Weak transcription	Aorta	Aorta
3	chr18:9479000-9533600	Weak transcription	Gastric	stomach
4	chr18:9495200-9530400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr18:9495200-9533600	Weak transcription	Right Ventricle	heart
6	chr18:9495400-9524000	Weak transcription	Spleen	Spleen
7	chr18:9495400-9534000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr18:9496800-9534000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr18:9497400-9532600	Weak transcription	Colonic Mucosa	Colon
10	chr18:9498400-9523200	Weak transcription	Esophagus	oesophagus
11	chr18:9499400-9525000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr18:9500800-9535000	Weak transcription	Fetal Heart	heart
13	chr18:9505200-9524600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr18:9506400-9522400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr18:9506800-9532000	Weak transcription	Pancreas	Pancrea
16	chr18:9507200-9522000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr18:9508000-9522400	Weak transcription	Lung	lung
18	chr18:9508000-9522600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr18:9508000-9531600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr18:9508400-9522400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr18:9508400-9522400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr18:9508600-9521800	Weak transcription	Ovary	ovary
23	chr18:9508600-9522000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr18:9508600-9525200	Weak transcription	Brain Germinal Matrix	brain
25	chr18:9508600-9531800	Weak transcription	Small Intestine	intestine
26	chr18:9509000-9522200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr18:9510800-9522200	Weak transcription	Fetal Lung	lung
28	chr18:9512000-9521800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr18:9512200-9524600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr18:9512800-9524400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr18:9513200-9524600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr18:9513200-9526600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr18:9513200-9534000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr18:9513600-9537800	Weak transcription	Fetal Brain Male	brain
35	chr18:9514200-9522200	Weak transcription	Fetal Intestine Small	intestine
36	chr18:9514200-9522400	Weak transcription	HSMMtube	muscle
37	chr18:9514200-9523200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr18:9514400-9521400	Weak transcription	Fetal Stomach	stomach
39	chr18:9514400-9521600	Weak transcription	HepG2	liver
40	chr18:9514400-9522600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr18:9514400-9524000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr18:9514600-9522000	Weak transcription	HMEC	breast
43	chr18:9514600-9524600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr18:9514600-9528800	Weak transcription	NH-A	brain
45	chr18:9514600-9530200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr18:9515400-9520400	Strong transcription	Dnd41	blood
47	chr18:9515600-9526800	Weak transcription	A549	lung
48	chr18:9515800-9522400	Weak transcription	Fetal Kidney	kidney
49	chr18:9516000-9522000	Weak transcription	Primary B cells from cord blood	blood
50	chr18:9516200-9521600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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