Variant report

Variant	rs11876171
Chromosome Location	chr18:9346578-9346579
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9341334..9344223-chr18:9346131..9348599,3	K562	blood:
2	chr18:9339033..9342733-chr18:9344110..9350817,6	K562	blood:
3	chr18:9334687..9337611-chr18:9345600..9347862,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128791	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1074159	0.83[ASN][1000 genomes]
rs10853376	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10853379	0.80[ASN][1000 genomes]
rs11081473	0.99[ASN][1000 genomes]
rs11081474	0.92[ASN][1000 genomes]
rs11873989	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11875585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11876202	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878159	0.84[ASN][1000 genomes]
rs11878163	0.83[ASN][1000 genomes]
rs12052039	0.81[ASN][1000 genomes]
rs12604438	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12956692	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12959183	0.83[ASN][1000 genomes]
rs12962014	1.00[ASN][1000 genomes]
rs12962166	0.83[ASN][1000 genomes]
rs12967229	0.86[ASN][1000 genomes]
rs1443594	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443595	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443599	0.98[ASN][1000 genomes]
rs1605473	0.82[ASN][1000 genomes]
rs1605474	0.81[ASN][1000 genomes]
rs1605476	0.86[ASN][1000 genomes]
rs2028654	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2028655	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2048146	0.83[ASN][1000 genomes]
rs2120317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298550	0.89[EUR][1000 genomes]
rs35584133	0.86[ASN][1000 genomes]
rs3786173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3859293	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4567794	1.00[ASN][1000 genomes]
rs4797362	0.81[ASN][1000 genomes]
rs4797366	0.81[ASN][1000 genomes]
rs4798794	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4798797	0.84[ASN][1000 genomes]
rs4798801	0.83[ASN][1000 genomes]
rs4798802	0.83[ASN][1000 genomes]
rs4798805	0.81[ASN][1000 genomes]
rs57524426	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62087478	0.84[ASN][1000 genomes]
rs6506652	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506653	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6506655	0.86[ASN][1000 genomes]
rs6506661	0.83[ASN][1000 genomes]
rs7228819	0.83[ASN][1000 genomes]
rs7230171	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7230328	0.84[ASN][1000 genomes]
rs7233925	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7234330	0.83[ASN][1000 genomes]
rs7234762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7236073	0.83[ASN][1000 genomes]
rs7236396	0.84[ASN][1000 genomes]
rs7237136	0.83[ASN][1000 genomes]
rs7237485	0.80[ASN][1000 genomes]
rs7237850	0.88[ASN][1000 genomes]
rs7239225	0.83[ASN][1000 genomes]
rs7240798	0.83[ASN][1000 genomes]
rs7242488	0.80[ASN][1000 genomes]
rs7243376	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7244054	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7245034	0.84[ASN][1000 genomes]
rs72948167	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8085920	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8087892	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8093045	0.84[ASN][1000 genomes]
rs8095060	0.95[ASN][1000 genomes]
rs8096911	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8096988	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8097654	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8097838	0.83[ASN][1000 genomes]
rs8099673	0.81[ASN][1000 genomes]
rs925100	0.99[ASN][1000 genomes]
rs9635818	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9635819	0.84[ASN][1000 genomes]
rs9635873	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs965280	0.83[ASN][1000 genomes]
rs9675975	0.83[ASN][1000 genomes]
rs9944562	0.83[ASN][1000 genomes]
rs9956536	0.98[ASN][1000 genomes]
rs9957701	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9959183	0.80[ASN][1000 genomes]
rs9963516	0.83[ASN][1000 genomes]
rs9966961	0.82[ASN][1000 genomes]
rs9967388	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv458023	chr18:9240413-9357786	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv576447	chr18:9240413-9357786	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv909365	chr18:9299538-9400422	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11876171	TWSG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9335400-9347800	Weak transcription	Small Intestine	intestine
2	chr18:9335400-9369400	Weak transcription	Pancreas	Pancrea
3	chr18:9335400-9371400	Weak transcription	Gastric	stomach
4	chr18:9335600-9366200	Weak transcription	Left Ventricle	heart
5	chr18:9335600-9372600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr18:9335800-9348000	Weak transcription	Psoas Muscle	Psoas
7	chr18:9335800-9348200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr18:9335800-9348400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr18:9335800-9348400	Weak transcription	Thymus	Thymus
10	chr18:9335800-9357600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr18:9335800-9366200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr18:9335800-9367600	Weak transcription	Fetal Thymus	thymus
13	chr18:9335800-9367600	Weak transcription	Lung	lung
14	chr18:9335800-9370200	Weak transcription	Adipose Nuclei	Adipose
15	chr18:9336000-9348000	Weak transcription	Hela-S3	cervix
16	chr18:9336000-9348400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr18:9336000-9348400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr18:9336000-9348600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr18:9336000-9355600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr18:9336000-9366200	Weak transcription	Brain Angular Gyrus	brain
21	chr18:9336200-9346800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr18:9336200-9347600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr18:9336200-9348000	Weak transcription	HepG2	liver
24	chr18:9336200-9348200	Weak transcription	HMEC	breast
25	chr18:9336200-9361400	Weak transcription	Aorta	Aorta
26	chr18:9336400-9349400	Weak transcription	Fetal Intestine Small	intestine
27	chr18:9337200-9346800	Strong transcription	Fetal Muscle Leg	muscle
28	chr18:9337600-9347600	Strong transcription	HSMM	muscle
29	chr18:9338200-9348200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr18:9338200-9354400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr18:9338400-9346600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr18:9338400-9348200	Weak transcription	K562	blood
33	chr18:9338400-9348200	Weak transcription	NHEK	skin
34	chr18:9338400-9348400	Weak transcription	Stomach Mucosa	stomach
35	chr18:9338400-9361600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr18:9338400-9366200	Weak transcription	Brain Anterior Caudate	brain
37	chr18:9338800-9348000	Weak transcription	Colon Smooth Muscle	Colon
38	chr18:9338800-9366000	Weak transcription	Brain Hippocampus Middle	brain
39	chr18:9339600-9347600	Weak transcription	HUVEC	blood vessel
40	chr18:9339600-9365600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr18:9340800-9346600	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr18:9341000-9371800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr18:9341200-9348000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr18:9341200-9348000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr18:9341200-9348400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr18:9341200-9361400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr18:9341200-9366400	Weak transcription	Brain Substantia Nigra	brain
48	chr18:9341200-9367400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr18:9341200-9391400	Weak transcription	Liver	Liver
50	chr18:9341200-9403800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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