Variant report

Variant	rs9834104
Chromosome Location	chr3:135692561-135692562
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	chr3:135683614..135686835-chr3:135692106..135694532,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073711	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10048942	0.84[ASN][1000 genomes]
rs10049233	0.84[ASN][1000 genomes]
rs10512981	0.93[ASN][1000 genomes]
rs10935175	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13072596	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082684	0.84[ASN][1000 genomes]
rs13097946	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098245	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325914	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434196	0.93[ASN][1000 genomes]
rs1403766	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1403770	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1523595	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523596	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523597	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1568349	0.93[ASN][1000 genomes]
rs1568350	0.80[EUR][1000 genomes]
rs16843509	0.93[ASN][1000 genomes]
rs17196987	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17197552	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17250445	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2204259	0.93[ASN][1000 genomes]
rs28449384	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28570106	0.81[EUR][1000 genomes]
rs28576629	0.84[ASN][1000 genomes]
rs34311570	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34409306	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34522617	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34767379	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35257855	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36039354	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4073308	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56807950	0.93[ASN][1000 genomes]
rs59063369	0.93[ASN][1000 genomes]
rs66544356	0.93[ASN][1000 genomes]
rs67039922	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771224	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771997	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773469	0.93[ASN][1000 genomes]
rs6774289	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775778	0.84[ASN][1000 genomes]
rs6779603	0.93[ASN][1000 genomes]
rs6786769	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802139	0.93[ASN][1000 genomes]
rs6807058	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6807242	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807565	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6809006	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810223	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71336046	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73222222	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7427833	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7433567	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7609938	0.93[ASN][1000 genomes]
rs7621331	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621396	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7621425	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626676	0.93[ASN][1000 genomes]
rs7628848	0.84[ASN][1000 genomes]
rs7638129	0.93[ASN][1000 genomes]
rs7640153	0.93[ASN][1000 genomes]
rs7641070	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7643661	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289502	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289503	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808979	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812561	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813082	0.93[ASN][1000 genomes]
rs9814557	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9819440	0.81[EUR][1000 genomes]
rs9819988	0.93[ASN][1000 genomes]
rs9820189	0.81[EUR][1000 genomes]
rs9824558	0.93[ASN][1000 genomes]
rs9825239	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9826806	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829329	0.93[ASN][1000 genomes]
rs9829476	0.93[ASN][1000 genomes]
rs9833799	0.93[ASN][1000 genomes]
rs9836374	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9836758	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9837355	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9839259	0.93[ASN][1000 genomes]
rs9842840	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842864	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9843725	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9844478	0.93[ASN][1000 genomes]
rs9846137	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848322	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9849088	0.93[ASN][1000 genomes]
rs9851361	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853577	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9862264	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862743	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9862763	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862777	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9864247	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9864514	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864656	0.93[ASN][1000 genomes]
rs9868246	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872542	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875328	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876837	0.93[ASN][1000 genomes]
rs9877082	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880721	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135685400-135692600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:135685600-135693800	Weak transcription	Gastric	stomach
3	chr3:135685800-135693800	Weak transcription	Lung	lung
4	chr3:135686600-135693400	Weak transcription	Right Ventricle	heart
5	chr3:135686600-135694400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:135686800-135692600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:135687000-135692800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:135687000-135692800	Weak transcription	Right Atrium	heart
9	chr3:135687000-135693200	Weak transcription	Fetal Lung	lung
10	chr3:135687000-135693200	Weak transcription	Fetal Stomach	stomach
11	chr3:135687200-135692600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:135687400-135692800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:135687400-135692800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:135687400-135692800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:135687400-135693400	Weak transcription	Left Ventricle	heart
16	chr3:135687600-135694000	Enhancers	Colon Smooth Muscle	Colon
17	chr3:135687600-135700400	Weak transcription	Fetal Intestine Small	intestine
18	chr3:135687800-135692600	Weak transcription	Fetal Heart	heart
19	chr3:135688000-135694200	Enhancers	Brain Hippocampus Middle	brain
20	chr3:135688400-135692800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:135688800-135694200	Enhancers	Brain Substantia Nigra	brain
22	chr3:135689400-135695200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr3:135689800-135692800	Weak transcription	NH-A	brain
24	chr3:135690000-135692600	Weak transcription	NHLF	lung
25	chr3:135690000-135692800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:135690000-135692800	Weak transcription	Aorta	Aorta
27	chr3:135690200-135692600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:135690200-135694200	Enhancers	Rectal Smooth Muscle	rectum
29	chr3:135690200-135701200	Weak transcription	NHEK	skin
30	chr3:135690200-135701400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:135690400-135692600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:135690400-135692800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:135690400-135694000	Weak transcription	HMEC	breast
34	chr3:135690400-135700800	Weak transcription	HSMM	muscle
35	chr3:135690600-135693200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:135690800-135692600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:135690800-135693000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:135690800-135693800	Weak transcription	NHDF-Ad	bronchial
39	chr3:135691000-135692600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:135691000-135699600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:135691200-135692600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:135691200-135692800	Weak transcription	Brain Anterior Caudate	brain
43	chr3:135691200-135693400	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr3:135691200-135699600	Weak transcription	Ovary	ovary
45	chr3:135691600-135694200	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr3:135691600-135694200	Enhancers	Brain Angular Gyrus	brain
47	chr3:135691600-135694400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr3:135691800-135693600	Enhancers	H1 Cell Line	embryonic stem cell
49	chr3:135691800-135693800	Enhancers	Stomach Mucosa	stomach
50	chr3:135692000-135693400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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