Variant report

Variant	rs9831977
Chromosome Location	chr3:52854140-52854141
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:52854140-52854290	WERI-Rb-1	eye:	n/a	n/a
2	CTCF	chr3:52854090-52854228	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52847640..52851112-chr3:52852588..52855076,3	MCF-7	breast:
2	chr3:52836954..52839305-chr3:52853241..52854782,2	K562	blood:

Variant related genes	Relation type
ITIH4	TF binding region
ITIH4-AS1	TF binding region
ENSG00000162267	Chromatin interaction
ENSG00000055955	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11130329	1.00[CHB][hapmap]
rs1139106	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11626	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11707829	1.00[CHB][hapmap]
rs11708390	1.00[CHB][hapmap]
rs11709430	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11712498	1.00[CHB][hapmap]
rs11713324	1.00[CHB][hapmap]
rs11717749	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11718060	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11720228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720233	1.00[CHB][hapmap]
rs13059141	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13076033	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs13080929	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17331151	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17331178	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2001732	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2071039	0.91[ASN][1000 genomes]
rs2240916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2240921	0.81[EUR][1000 genomes]
rs2276818	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2276822	1.00[JPT][hapmap]
rs28552648	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs33999310	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34288509	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34860124	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755801	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3755805	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3796352	1.00[CHB][hapmap]
rs4687676	1.00[ASN][1000 genomes]
rs6798472	1.00[CHB][hapmap]
rs9968117	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9831977	TMEM110	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52844200-52856600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:52844400-52857200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:52844600-52856800	Weak transcription	Fetal Intestine Small	intestine
4	chr3:52844600-52857600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:52845800-52854200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:52846400-52860800	Weak transcription	Esophagus	oesophagus
7	chr3:52846800-52857000	Weak transcription	Aorta	Aorta
8	chr3:52847000-52857400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:52847200-52861200	Genic enhancers	Liver	Liver
10	chr3:52847400-52857000	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:52847600-52865000	Weak transcription	Psoas Muscle	Psoas
12	chr3:52847800-52854600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:52848400-52865800	Weak transcription	Ovary	ovary
14	chr3:52848800-52854200	Weak transcription	Brain Substantia Nigra	brain
15	chr3:52850200-52868400	Weak transcription	Colonic Mucosa	Colon
16	chr3:52850600-52857800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:52850600-52864200	Strong transcription	Stomach Smooth Muscle	stomach
18	chr3:52850800-52865400	Strong transcription	Fetal Stomach	stomach
19	chr3:52851000-52856800	Weak transcription	Fetal Brain Female	brain
20	chr3:52851200-52855400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:52851600-52863400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:52851800-52855200	Strong transcription	Brain Anterior Caudate	brain
23	chr3:52851800-52856800	Weak transcription	Lung	lung
24	chr3:52851800-52858000	Weak transcription	Placenta	Placenta
25	chr3:52852200-52869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr3:52852400-52854200	Genic enhancers	Fetal Thymus	thymus
27	chr3:52852400-52854400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr3:52852800-52854800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:52852800-52869200	Weak transcription	Primary B cells from cord blood	blood
30	chr3:52853000-52854400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr3:52853000-52854400	Strong transcription	Brain Germinal Matrix	brain
32	chr3:52853000-52857000	Weak transcription	Gastric	stomach
33	chr3:52853000-52857000	Enhancers	HepG2	liver
34	chr3:52853000-52857000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr3:52853000-52858400	Strong transcription	Brain Angular Gyrus	brain
36	chr3:52853000-52868000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:52853200-52855600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
38	chr3:52853200-52859400	Strong transcription	Thymus	Thymus
39	chr3:52853400-52854400	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr3:52853400-52856600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:52853400-52857600	Strong transcription	Spleen	Spleen
42	chr3:52853400-52861200	Strong transcription	Fetal Muscle Leg	muscle
43	chr3:52853600-52854200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:52853600-52854400	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr3:52853600-52854400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:52853600-52854800	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr3:52853600-52855200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:52853600-52855600	Enhancers	Fetal Muscle Trunk	muscle
49	chr3:52853800-52855000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
50	chr3:52853800-52855800	Strong transcription	Right Ventricle	heart

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