Variant report

Variant	rs3772108
Chromosome Location	chr3:196005189-196005190
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:196002832..196006454-chr3:196043671..196046780,4	MCF-7	breast:
2	chr3:196005160..196007960-chr3:196014818..196016357,2	K562	blood:

Variant related genes	Relation type
ENSG00000213123	Chromatin interaction
ENSG00000235897	Chromatin interaction
ENSG00000272741	Chromatin interaction
ENSG00000161217	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12632779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12633454	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12633827	0.85[ASN][1000 genomes]
rs12634350	0.85[ASN][1000 genomes]
rs12634587	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12635925	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1357290	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3772107	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4396926	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56701784	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57987393	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58297632	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58568267	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs58845625	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59289255	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59708858	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60167422	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61254593	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61588443	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66935510	0.89[ASN][1000 genomes]
rs67199839	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72611187	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72611188	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72611189	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72611190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73212156	0.82[ASN][1000 genomes]
rs7617236	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7635355	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
7	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
8	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
9	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
10	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
11	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
13	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
14	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
15	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
16	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
17	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
18	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
19	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
20	nsv518925	chr3:196002067-196005444	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3772108	TCTEX1D2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195965800-196012400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:195969600-196012400	Weak transcription	Fetal Brain Male	brain
3	chr3:195990400-196006400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:195991800-196012400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:195993000-196005200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:195995400-196005200	Weak transcription	A549	lung
7	chr3:195996200-196005200	Weak transcription	HUVEC	blood vessel
8	chr3:195996600-196006200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:195996600-196012600	Weak transcription	Fetal Kidney	kidney
10	chr3:195997400-196006200	Weak transcription	HSMM	muscle
11	chr3:195997400-196006400	Weak transcription	Brain Angular Gyrus	brain
12	chr3:195997600-196007800	Weak transcription	Small Intestine	intestine
13	chr3:195997600-196010600	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:195997800-196006200	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:196000000-196005800	Weak transcription	Pancreas	Pancrea
16	chr3:196000200-196005200	Weak transcription	Psoas Muscle	Psoas
17	chr3:196000200-196006200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:196000400-196005400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:196000400-196006400	Weak transcription	HSMMtube	muscle
20	chr3:196000600-196005200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:196000600-196006200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:196000600-196006200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:196000600-196006200	Weak transcription	Colonic Mucosa	Colon
24	chr3:196000600-196011200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:196000600-196012400	Weak transcription	Fetal Brain Female	brain
26	chr3:196000600-196012600	Weak transcription	Fetal Lung	lung
27	chr3:196000600-196012800	Weak transcription	Ovary	ovary
28	chr3:196000600-196013800	Weak transcription	Aorta	Aorta
29	chr3:196000800-196005200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:196000800-196006200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:196001000-196005200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:196001000-196006200	Weak transcription	Brain Substantia Nigra	brain
33	chr3:196001000-196011600	Weak transcription	Thymus	Thymus
34	chr3:196001000-196013800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:196001200-196005200	Weak transcription	Left Ventricle	heart
36	chr3:196001200-196005600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:196001200-196006200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:196001200-196006200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:196001200-196011400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:196001200-196013600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:196001400-196005200	Weak transcription	Placenta	Placenta
42	chr3:196001400-196005400	Weak transcription	Fetal Muscle Leg	muscle
43	chr3:196001400-196005400	Weak transcription	Right Atrium	heart
44	chr3:196001400-196005600	Weak transcription	Fetal Thymus	thymus
45	chr3:196001400-196005600	Weak transcription	Lung	lung
46	chr3:196001400-196005800	Weak transcription	Right Ventricle	heart
47	chr3:196001400-196006200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:196001400-196006400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:196001400-196013000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:196001400-196013200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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